This worksheet is intended to gather annotation data for use when looking at tnseq analyses of S.pyogenes strain 5448. The analyses were performed in July 2017, but I am re-running them in 2018 to make sure that all the code still works.
There are a few methods of importing annotation data into R. The following illustrate some of them.
The function load_genbank_annotations() should download the .gb file from genbank, read it, and provide a set of data frames which are useful.
mgas_data <- sm(load_genbank_annotations(accession="CP008776"))
genome_size <- GenomicRanges::width(mgas_data$seq) ## This fails on travis?
mgas_cds <- as.data.frame(mgas_data$cds)
## Get rid of amino acid sequence
mgas_cds <- mgas_cds[-15]
mgas_cds <- mgas_cds[-16]
rownames(mgas_cds) <- mgas_cds[["locus_tag"]]
summary(mgas_data)## Length Class Mode
## others 82 GRanges S4
## exons 1723 GRanges S4
## cds 1723 GRanges S4
## genes 1814 GRanges S4
## txdb 1 TxDb S4
## seq 1 DNAStringSet S4nc_features <- as.data.frame(mgas_data$others)
write.csv(nc_features, file="nc_features.csv")
cds_features <- as.data.frame(mgas_data$cds)
write.csv(cds_features, file="cds_features.csv")Another source of good annotation data for bacterial species is microbesonline. Its only real annoyance is that it has a whole new set of identifiers for the various species it contains, and my function which gathers them apparently caused it to throw errors internally. Thus, in order to get the genome ID, I need to go to microbesonline.org and ask it explicitly; ergo the arbitrary number below.
##microbe_ids <- get_microbesonline_ids("pyogenes")
##microbe_ids
microbe_ids <- 293653 ## MGAS5005
mgas_df <- load_microbesonline_annotations(microbe_ids)In contrast, it is possible to load most annotations of interest directly from the gff files used in the alignments. More in-depth information for the human transcriptome may be extracted from biomart.
## The old way of getting genome/annotation data
sp_gff <- "reference/mgas_5448.gff"
sp_fasta <- "reference/mgas_5448.fasta"
sp_annotations <- load_gff_annotations(sp_gff, type="gene")We have some annotations and will now create an expt containing the annotations and count data.
The create_expt() function brings together the annotation data, the count tables in the sample sheet, and the metadata in the sample sheet into a canonical R expressionSet. It then adds a small amount of extra information (sample colors, for example), and recasts it as an expt.
sp_expt <- sm(create_expt(metadata="sample_sheets/samples_v3.xlsx", gene_info=mgas_cds))
knitr::kable(pData(sp_expt))| sampleid | samplename | runnumber | condition | time | cu | zn | cuzn | medium | coverage | replicate | batch | experiment | description | startdate | pathogen | strain | experimentdescription | x19 | barcode | barcodesequence | file | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HPGL0864 | HPGL0864 | Lane 6, Index 505 (AGGCGAAG) | 07 | thy_t1 | t1 | optimal | optimal | optimal_optimal | thy | c05 | r1 | b | metal homeostasis | AGT41_THY_T1_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T1, sample 1 | lane 6 | 505 | AGGCGAAG | preprocessing/hpgl0864/outputs/bowtie_mgas_5448/hpgl0864-v0M1_v0M1.count.xz |
| HPGL0865 | HPGL0865 | Lane 6, Index506 (TAATCTTA) | 07 | thy_t1 | t1 | optimal | optimal | optimal_optimal | thy | c05 | r2 | b | metal homeostasis | AGT42_THY_T1_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T1, sample 2 | lane 6 | 506 | TAATCTTA | preprocessing/hpgl0865/outputs/bowtie_mgas_5448/hpgl0865-v0M1_v0M1.count.xz |
| HPGL0866 | HPGL0866 | Lane 1, Index 501 (TATAGCCT) | 05 | rpmi_t2 | t2 | optimal | optimal | optimal_optimal | rpmi | c03 | r1 | b | metal homeostasis | AGT1_mRPMI_T2_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, sample 1 | lane 1 | 501 | TATAGCCT | preprocessing/hpgl0866/outputs/bowtie_mgas_5448/hpgl0866-v0M1_v0M1.count.xz |
| HPGL0867 | HPGL0867 | Lane 1, Index506 (TAATCTTA) | 05 | rpmi_t2 | t2 | optimal | optimal | optimal_optimal | rpmi | c04 | r2 | b | metal homeostasis | AGT6_mRPMI_T2_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, sample 2 | lane 1 | 506 | TAATCTTA | preprocessing/hpgl0867/outputs/bowtie_mgas_5448/hpgl0867-v0M1_v0M1.count.xz |
| HPGL0868 | HPGL0868 | Lane 2, Index 703 (CGCTCATT) | 05 | rpmi_t2 | t2 | optimal | optimal | optimal_optimal | rpmi | c03 | r3 | b | metal homeostasis | AGT11_mRPMI_T2_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, sample 3 | lane 2 | 703 | CGCTCATT | preprocessing/hpgl0868/outputs/bowtie_mgas_5448/hpgl0868-v0M1_v0M1.count.xz |
| HPGL0869 | HPGL0869 | Lane 2, Index 504 (GGCTCTGA) | 05 | rpmi_t2 | t2 | optimal | optimal | optimal_optimal | rpmi | c03 | r4 | b | metal homeostasis | AGT16_mRPMI_T2_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, sample 4 | lane 2 | 504 | GGCTCTGA | preprocessing/hpgl0869/outputs/bowtie_mgas_5448/hpgl0869-v0M1_v0M1.count.xz |
| HPGL0870 | HPGL0870 | Lane 1, Index 502 ( ATAGAGGC) | 05 | rpmi_t2_lowcu | t2 | low | optimal | low_optimal | rpmi | c06 | r1 | b | metal homeostasis | AGT2_mRPMI_T2_lowCu_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowCu, sample 1 | lane 1 | 502 | ATAGAGGC | preprocessing/hpgl0870/outputs/bowtie_mgas_5448/hpgl0870-v0M1_v0M1.count.xz |
| HPGL0871 | HPGL0871 | Lane 1, Index 507 (CAGGACGT) | 05 | rpmi_t2_lowcu | t2 | low | optimal | low_optimal | rpmi | c03 | r2 | b | metal homeostasis | AGT7_mRPMI_T2_lowCu_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowCu, sample 2 | lane 1 | 507 | CAGGACGT | preprocessing/hpgl0871/outputs/bowtie_mgas_5448/hpgl0871-v0M1_v0M1.count.xz |
| HPGL0872 | HPGL0872 | Lane 2, Index 704 (GAGATTCC) | 05 | rpmi_t2_lowcu | t2 | low | optimal | low_optimal | rpmi | c08 | r3 | b | metal homeostasis | AGT12_mRPMI_T2_lowCu_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowCu, sample 3 | lane 2 | 704 | GAGATTCC | preprocessing/hpgl0872/outputs/bowtie_mgas_5448/hpgl0872-v0M1_v0M1.count.xz |
| HPGL0873 | HPGL0873 | Lane 3, Index 505 (AGGCGAAG) | 06 | rpmi_t2_lowcu | t2 | low | optimal | low_optimal | rpmi | c04 | r4 | b | metal homeostasis | AGT17_mRPMI_T2_lowCu_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowCu, sample 4 | lane 3 | 505 | AGGCGAAG | preprocessing/hpgl0873/outputs/bowtie_mgas_5448/hpgl0873-v0M1_v0M1.count.xz |
| HPGL0874 | HPGL0874 | Lane 1, Index 503 (CCTATCCT) | 05 | rpmi_t2_highcu | t2 | high | optimal | high_optimal | rpmi | c03 | r1 | b | metal homeostasis | AGT3_mRPMI_T2_highCu_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highCu, sample 1 | lane 1 | 503 | CCTATCCT | preprocessing/hpgl0874/outputs/bowtie_mgas_5448/hpgl0874-v0M1_v0M1.count.xz |
| HPGL0875 | HPGL0875 | Lane 1, Index 508 (GTACTGAC) | 05 | rpmi_t2_highcu | t2 | high | optimal | high_optimal | rpmi | c05 | r2 | b | metal homeostasis | AGT8_mRPMI_T2_highCu_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highCu, sample 2 | lane 1 | 508 | GTACTGAC | preprocessing/hpgl0875/outputs/bowtie_mgas_5448/hpgl0875-v0M1_v0M1.count.xz |
| HPGL0876 | HPGL0876 | Lane 2, Index 501 (TATAGCCT) | 05 | rpmi_t2_highcu | t2 | high | optimal | high_optimal | rpmi | c10 | r3 | b | metal homeostasis | AGT13_mRPMI_T2_highCu_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highCu, sample 3 | lane 2 | 501 | TATAGCCT | preprocessing/hpgl0876/outputs/bowtie_mgas_5448/hpgl0876-v0M1_v0M1.count.xz |
| HPGL0877 | HPGL0877 | Lane 3, Index506 (TAATCTTA) | 06 | rpmi_t2_highcu | t2 | high | optimal | high_optimal | rpmi | c06 | r4 | b | metal homeostasis | AGT18_mRPMI_T2_highCu_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highCu, sample 4 | lane 3 | 506 | TAATCTTA | preprocessing/hpgl0877/outputs/bowtie_mgas_5448/hpgl0877-v0M1_v0M1.count.xz |
| HPGL0878 | HPGL0878 | Lane 1, Index 504 (GGCTCTGA) | 05 | rpmi_t2_lowzn | t2 | optimal | low | optimal_low | rpmi | c03 | r1 | b | metal homeostasis | AGT4_mRPMI_T2_lowZn_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowZn, sample 1 | lane 1 | 504 | GGCTCTGA | preprocessing/hpgl0878/outputs/bowtie_mgas_5448/hpgl0878-v0M1_v0M1.count.xz |
| HPGL0879 | HPGL0879 | Lane 2, Index 701 (ATTACTCG) | 05 | rpmi_t2_lowzn | t2 | optimal | low | optimal_low | rpmi | c01 | r2 | b | metal homeostasis | AGT9_mRPMI_T2_lowZn_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowZn, sample 2 | lane 2 | 701 | ATTACTCGG | preprocessing/hpgl0879/outputs/bowtie_mgas_5448/hpgl0879-v0M1_v0M1.count.xz |
| HPGL0880 | HPGL0880 | Lane 2, Index 502 (ATAGAGGC) | 05 | rpmi_t2_lowzn | t2 | optimal | low | optimal_low | rpmi | c05 | r3 | b | metal homeostasis | AGT14_mRPMI_T2_lowZn_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowZn, sample 3 | lane 2 | 502 | ATAGAGGC | preprocessing/hpgl0880/outputs/bowtie_mgas_5448/hpgl0880-v0M1_v0M1.count.xz |
| HPGL0881 | HPGL0881 | Lane 3, Index 507 (CAGGACGT) | 06 | rpmi_t2_lowzn | t2 | optimal | low | optimal_low | rpmi | c04 | r4 | b | metal homeostasis | AGT19_mRPMI_T2_lowZn_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, lowZn, sample 4 | lane 3 | 507 | CAGGACGT | preprocessing/hpgl0881/outputs/bowtie_mgas_5448/hpgl0881-v0M1_v0M1.count.xz |
| HPGL0882 | HPGL0882 | Lane 1, Index 505 (AGGCGAAG) | 05 | rpmi_t2_highzn | t2 | optimal | high | optimal_high | rpmi | c05 | r1 | b | metal homeostasis | AGT5_mRPMI_T2_highZn_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highZn, sample 1 | lane 1 | 505 | AGGCGAAG | preprocessing/hpgl0882/outputs/bowtie_mgas_5448/hpgl0882-v0M1_v0M1.count.xz |
| HPGL0883 | HPGL0883 | Lane 2, Index 702 (TCCGGAGA) | 05 | rpmi_t2_highzn | t2 | optimal | high | optimal_high | rpmi | c07 | r2 | b | metal homeostasis | AGT10_mRPMI_T2_highZn_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highZn, sample 2 | lane 2 | 702 | TCCGGAGA | preprocessing/hpgl0883/outputs/bowtie_mgas_5448/hpgl0883-v0M1_v0M1.count.xz |
| HPGL0884 | HPGL0884 | Lane 2, Index 503 (CCTATCCT) | 05 | rpmi_t2_highzn | t2 | optimal | high | optimal_high | rpmi | c07 | r3 | b | metal homeostasis | AGT15_mRPMI_T2_highZn_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highZn, sample 3 | lane 2 | 503 | CCTATCCT | preprocessing/hpgl0884/outputs/bowtie_mgas_5448/hpgl0884-v0M1_v0M1.count.xz |
| HPGL0885 | HPGL0885 | Lane 3, Index 508 (GTACTGAC) | 06 | rpmi_t2_highzn | t2 | optimal | high | optimal_high | rpmi | c08 | r4 | b | metal homeostasis | AGT20_mRPMI_T2_highZn_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T2, highZn, sample 4 | lane 3 | 508 | GTACTGAC | preprocessing/hpgl0885/outputs/bowtie_mgas_5448/hpgl0885-v0M1_v0M1.count.xz |
| HPGL0886 | HPGL0886 | Lane 3, Index 701 (ATTACTCG) | 06 | rpmi_t3 | t3 | optimal | optimal | optimal_optimal | rpmi | c05 | r1 | b | metal homeostasis | AGT21_mRPMI_T3_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, sample 1 | lane 3 | 701 | ATTACTCGG | preprocessing/hpgl0886/outputs/bowtie_mgas_5448/hpgl0886-v0M1_v0M1.count.xz |
| HPGL0887 | HPGL0887 | Lane 4, Index 502 (ATAGAGGC) | 06 | rpmi_t3 | t3 | optimal | optimal | optimal_optimal | rpmi | c03 | r2 | b | metal homeostasis | AGT26_mRPMI_T3_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, sample 2 | lane 4 | 502 | ATAGAGGC | preprocessing/hpgl0887/outputs/bowtie_mgas_5448/hpgl0887-v0M1_v0M1.count.xz |
| HPGL0888 | HPGL0888 | Lane 4, Index 507 (CAGGACGT) | 06 | rpmi_t3 | t3 | optimal | optimal | optimal_optimal | rpmi | c02 | r3 | b | metal homeostasis | AGT31_mRPMI_T3_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, sample 3 | lane 4 | 507 | CAGGACGT | preprocessing/hpgl0888/outputs/bowtie_mgas_5448/hpgl0888-v0M1_v0M1.count.xz |
| HPGL0889 | HPGL0889 | Lane 5, Index 704 (GAGATTCC) | 07 | rpmi_t3 | t3 | optimal | optimal | optimal_optimal | rpmi | c05 | r4 | b | metal homeostasis | AGT36_mRPMI_T3_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, sample 4 | lane 5 | 704 | GAGATTCC | preprocessing/hpgl0889/outputs/bowtie_mgas_5448/hpgl0889-v0M1_v0M1.count.xz |
| HPGL0890 | HPGL0890 | Lane 3, Index 702 (TCCGGAGA) | 06 | rpmi_t3_lowcu | t3 | low | optimal | low_optimal | rpmi | c08 | r1 | b | metal homeostasis | AGT22_mRPMI_T3_lowCu_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowCu, sample 1 | lane 3 | 702 | TCCGGAGA | preprocessing/hpgl0890/outputs/bowtie_mgas_5448/hpgl0890-v0M1_v0M1.count.xz |
| HPGL0891 | HPGL0891 | Lane 4, Index 503 (CCTATCCT) | 06 | rpmi_t3_lowcu | t3 | low | optimal | low_optimal | rpmi | c03 | r2 | b | metal homeostasis | AGT27_mRPMI_T3_lowCu_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowCu, sample 2 | lane 4 | 503 | CCTATCCT | preprocessing/hpgl0891/outputs/bowtie_mgas_5448/hpgl0891-v0M1_v0M1.count.xz |
| HPGL0892 | HPGL0892 | Lane 4, Index 508 (GTACTGAC) | 06 | rpmi_t3_lowcu | t3 | low | optimal | low_optimal | rpmi | c03 | r3 | b | metal homeostasis | AGT32_mRPMI_T3_lowCu_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowCu, sample 3 | lane 4 | 508 | GTACTGAC | preprocessing/hpgl0892/outputs/bowtie_mgas_5448/hpgl0892-v0M1_v0M1.count.xz |
| HPGL0893 | HPGL0893 | Lane 5, Index 501 (TATAGCCT) | 07 | rpmi_t3_lowcu | t3 | low | optimal | low_optimal | rpmi | c04 | r4 | b | metal homeostasis | AGT37_mRPMI_T3_lowCu_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowCu, sample 4 | lane 5 | 501 | TATAGCCT | preprocessing/hpgl0893/outputs/bowtie_mgas_5448/hpgl0893-v0M1_v0M1.count.xz |
| HPGL0894 | HPGL0894 | Lane 3, Index 703 (CGCTCATT) | 06 | rpmi_t3_highcu | t3 | high | optimal | high_optimal | rpmi | c08 | r1 | b | metal homeostasis | AGT23_mRPMI_T3_highCu_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highCu, sample 1 | lane 3 | 703 | CGCTCATT | preprocessing/hpgl0894/outputs/bowtie_mgas_5448/hpgl0894-v0M1_v0M1.count.xz |
| HPGL0895 | HPGL0895 | Lane 4, Index 504 (GGCTCTGA) | 06 | rpmi_t3_highcu | t3 | high | optimal | high_optimal | rpmi | c05 | r2 | b | metal homeostasis | AGT28_mRPMI_T3_highCu_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highCu, sample 2 | lane 4 | 504 | GGCTCTGA | preprocessing/hpgl0895/outputs/bowtie_mgas_5448/hpgl0895-v0M1_v0M1.count.xz |
| HPGL0896 | HPGL0896 | Lane 5, Index 701 (ATTACTCG) | 07 | rpmi_t3_highcu | t3 | high | optimal | high_optimal | rpmi | c06 | r3 | b | metal homeostasis | AGT33_mRPMI_T3_highCu_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highCu, sample 3 | lane 5 | 701 | ATTACTCGG | preprocessing/hpgl0896/outputs/bowtie_mgas_5448/hpgl0896-v0M1_v0M1.count.xz |
| HPGL0897 | HPGL0897 | Lane 5, Index 502 (ATAGAGGC) | 07 | rpmi_t3_highcu | t3 | high | optimal | high_optimal | rpmi | c04 | r4 | b | metal homeostasis | AGT38_mRPMI_T3_highCu_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highCu, sample 4 | lane 5 | 502 | ATAGAGGC | preprocessing/hpgl0897/outputs/bowtie_mgas_5448/hpgl0897-v0M1_v0M1.count.xz |
| HPGL0898 | HPGL0898 | Lane 3, Index 704 (GAGATTCC) | 06 | rpmi_t3_lowzn | t3 | optimal | low | optimal_low | rpmi | c01 | r1 | b | metal homeostasis | AGT24_mRPMI_T3_lowZn_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowZn, sample 1 | lane 3 | 704 | GAGATTCC | preprocessing/hpgl0898/outputs/bowtie_mgas_5448/hpgl0898-v0M1_v0M1.count.xz |
| HPGL0899 | HPGL0899 | Lane 4, Index 505 (AGGCGAAG) | 06 | rpmi_t3_lowzn | t3 | optimal | low | optimal_low | rpmi | c04 | r2 | b | metal homeostasis | AGT29_mRPMI_T3_lowZn_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowZn, sample 2 | lane 4 | 505 | AGGCGAAG | preprocessing/hpgl0899/outputs/bowtie_mgas_5448/hpgl0899-v0M1_v0M1.count.xz |
| HPGL0900 | HPGL0900 | Lane 5, Index 702 (TCCGGAGA) | 07 | rpmi_t3_lowzn | t3 | optimal | low | optimal_low | rpmi | c06 | r3 | b | metal homeostasis | AGT34_mRPMI_T3_lowZn_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowZn, sample 3 | lane 5 | 702 | TCCGGAGA | preprocessing/hpgl0900/outputs/bowtie_mgas_5448/hpgl0900-v0M1_v0M1.count.xz |
| HPGL0901 | HPGL0901 | Lane 5, Index 503 (CCTATCCT) | 07 | rpmi_t3_lowzn | t3 | optimal | low | optimal_low | rpmi | c04 | r4 | b | metal homeostasis | AGT39_mRPMI_T3_lowZn_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, lowZn, sample 4 | lane 5 | 503 | CCTATCCT | preprocessing/hpgl0901/outputs/bowtie_mgas_5448/hpgl0901-v0M1_v0M1.count.xz |
| HPGL0902 | HPGL0902 | Lane 4, Index 501 (TATAGCCT) | 06 | rpmi_t3_highzn | t3 | optimal | high | optimal_high | rpmi | c03 | r1 | b | metal homeostasis | AGT25_mRPMI_T3_highZn_replicate1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highZn, sample 1 | lane 4 | 501 | TATAGCCT | preprocessing/hpgl0902/outputs/bowtie_mgas_5448/hpgl0902-v0M1_v0M1.count.xz |
| HPGL0903 | HPGL0903 | Lane 4, Index506 (TAATCTTA) | 06 | rpmi_t3_highzn | t3 | optimal | high | optimal_high | rpmi | c04 | r2 | b | metal homeostasis | AGT30_mRPMI_T3_highZn_replicate2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highZn, sample 2 | lane 4 | 506 | TAATCTTA | preprocessing/hpgl0903/outputs/bowtie_mgas_5448/hpgl0903-v0M1_v0M1.count.xz |
| HPGL0904 | HPGL0904 | Lane 5, Index 703 (CGCTCATT) | 07 | rpmi_t3_highzn | t3 | optimal | high | optimal_high | rpmi | c02 | r3 | b | metal homeostasis | AGT35_mRPMI_T3_highZn_replicate3 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highZn, sample 3 | lane 5 | 703 | CGCTCATT | preprocessing/hpgl0904/outputs/bowtie_mgas_5448/hpgl0904-v0M1_v0M1.count.xz |
| HPGL0905 | HPGL0905 | Lane 5, Index 504 (GGCTCTGA) | 07 | rpmi_t3_highzn | t3 | optimal | high | optimal_high | rpmi | c04 | r4 | b | metal homeostasis | AGT40_mRPMI_T3_highZn_replicate4 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448, T3, highZn, sample 4 | lane 5 | 504 | GGCTCTGA | preprocessing/hpgl0905/outputs/bowtie_mgas_5448/hpgl0905-v0M1_v0M1.count.xz |
| HPGL0906 | HPGL0906 | Lane 6, Index 507 (CAGGACGT) | 07 | ap_t1 | t1 | optimal | optimal | optimal_optimal | thy | NA | NA | a | Krmit in 5448AP | YLB1_Library5448AP_2_T1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448AP, Library 2, T1 | lane 6 | 507 | CAGGACGT | preprocessing/hpgl0906/outputs/bowtie_mgas_5448/hpgl0906-v0M1_v0M1.count.xz |
| HPGL0907 | HPGL0907 | Lane 6, Index 508 (GTACTGAC) | 07 | ap_t1 | t1 | optimal | optimal | optimal_optimal | thy | NA | NA | a | Krmit in 5448AP | YLB2_Library5448AP_10_T1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448AP, Library 10, T1 | lane 6 | 508 | GTACTGAC | preprocessing/hpgl0907/outputs/bowtie_mgas_5448/hpgl0907-v0M1_v0M1.count.xz |
| HPGL0908 | HPGL0908 | Lane 6, Index 701 (ATTACTCG) | 07 | ap_t1 | t1 | optimal | optimal | optimal_optimal | thy | NA | NA | a | Krmit in 5448AP | YLB3_Library5448AP_12_T1 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448AP, Library 12, T1 | lane 6 | 701 | ATTACTCGG | preprocessing/hpgl0908/outputs/bowtie_mgas_5448/hpgl0908-v0M1_v0M1.count.xz |
| HPGL0909 | HPGL0909 | Lane 6, Index 702 (TCCGGAGA) | 07 | ap_t2 | t2 | optimal | optimal | optimal_optimal | thy | NA | NA | a | Krmit in 5448AP | YLB4_Library5448AP_2_T2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448AP, Library 2, T2 | lane 6 | 702 | TCCGGAGA | preprocessing/hpgl0909/outputs/bowtie_mgas_5448/hpgl0909-v0M1_v0M1.count.xz |
| HPGL0910 | HPGL0910 | Lane 6, Index 703 (CGCTCATT) | 07 | ap_t2 | t2 | optimal | optimal | optimal_optimal | thy | NA | NA | a | Krmit in 5448AP | YLB5_Library5448AP_10_T2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448AP, Library 10, T2 | lane 6 | 703 | CGCTCATT | preprocessing/hpgl0910/outputs/bowtie_mgas_5448/hpgl0910-v0M1_v0M1.count.xz |
| HPGL0911 | HPGL0911 | Lane 6, Index 704 (GAGATTCC) | 07 | ap_t2 | t2 | optimal | optimal | optimal_optimal | thy | NA | NA | a | Krmit in 5448AP | YLB6_Library5448AP_12_T2 | 2017-05 | S.pyogenes | 5448 | Krmit in 5448AP, Library 12, T2 | lane 6 | 704 | GAGATTCC | preprocessing/hpgl0911/outputs/bowtie_mgas_5448/hpgl0911-v0M1_v0M1.count.xz |
message(paste0("This is hpgltools commit: ", get_git_commit()))## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset c730ef178f8e57bbf3819e21cf5e6cfe879e6328## R> packrat::restore()## This is hpgltools commit: Fri Jul 13 17:21:39 2018 -0400: c730ef178f8e57bbf3819e21cf5e6cfe879e6328pander::pander(sessionInfo())R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.utf8, LC_NUMERIC=C, LC_TIME=en_US.utf8, LC_COLLATE=en_US.utf8, LC_MONETARY=en_US.utf8, LC_MESSAGES=en_US.utf8, LC_PAPER=en_US.utf8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.utf8 and LC_IDENTIFICATION=C
attached base packages: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: hpgltools(v.2018.03)
loaded via a namespace (and not attached): Biobase(v.2.40.0), httr(v.1.3.1), jsonlite(v.1.5), bit64(v.0.9-7), foreach(v.1.4.4), assertthat(v.0.2.0), highr(v.0.7), stats4(v.3.5.1), pander(v.0.6.2), blob(v.1.1.1), BSgenome(v.1.48.0), GenomeInfoDbData(v.1.1.0), Rsamtools(v.1.32.2), yaml(v.2.1.19), progress(v.1.2.0), pillar(v.1.3.0), RSQLite(v.2.1.1), backports(v.1.1.2), lattice(v.0.20-35), glue(v.1.2.0), digest(v.0.6.15), RColorBrewer(v.1.1-2), GenomicRanges(v.1.32.4), XVector(v.0.20.0), colorspace(v.1.3-2), htmltools(v.0.3.6), Matrix(v.1.2-14), plyr(v.1.8.4), XML(v.3.98-1.12), pkgconfig(v.2.0.1), devtools(v.1.13.6), biomaRt(v.2.36.1), zlibbioc(v.1.26.0), purrr(v.0.2.5), scales(v.0.5.0), openxlsx(v.4.1.0), BiocParallel(v.1.14.2), tibble(v.1.4.2), IRanges(v.2.14.10), ggplot2(v.3.0.0), withr(v.2.1.2), SummarizedExperiment(v.1.10.1), GenomicFeatures(v.1.32.0), BiocGenerics(v.0.26.0), lazyeval(v.0.2.1), magrittr(v.1.5), crayon(v.1.3.4), memoise(v.1.1.0), evaluate(v.0.10.1), xml2(v.1.2.0), tools(v.3.5.1), data.table(v.1.11.4), prettyunits(v.1.0.2), hms(v.0.4.2), matrixStats(v.0.53.1), stringr(v.1.3.1), S4Vectors(v.0.18.3), munsell(v.0.5.0), zip(v.1.0.0), DelayedArray(v.0.6.1), genbankr(v.1.8.0), AnnotationDbi(v.1.42.1), bindrcpp(v.0.2.2), Biostrings(v.2.48.0), compiler(v.3.5.1), GenomeInfoDb(v.1.16.0), rlang(v.0.2.1), grid(v.3.5.1), RCurl(v.1.95-4.11), iterators(v.1.0.10), VariantAnnotation(v.1.26.1), bitops(v.1.0-6), base64enc(v.0.1-3), rmarkdown(v.1.10), rentrez(v.1.2.1), gtable(v.0.2.0), codetools(v.0.2-15), curl(v.3.2), DBI(v.1.0.0), roxygen2(v.6.0.1), R6(v.2.2.2), GenomicAlignments(v.1.16.0), knitr(v.1.20), dplyr(v.0.7.6), rtracklayer(v.1.40.3), bit(v.1.1-14), bindr(v.0.1.1), commonmark(v.1.5), rprojroot(v.1.3-2), stringi(v.1.2.3), parallel(v.3.5.1), Rcpp(v.0.12.17) and tidyselect(v.0.2.4)
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))## Saving to 01_annotation-v20180717.rda.xztt <- sm(saveme(filename=this_save))