Last updated: 2019-10-16
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Knit directory: Comparative_APA/analysis/
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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a255e22 | brimittleman | 2019-10-16 | add code and annotations for dt plots |
| html | 4ea2576 | brimittleman | 2019-10-04 | Build site. |
| Rmd | 920abac | brimittleman | 2019-10-04 | add comaprison to old PAS |
| html | 7ec7862 | brimittleman | 2019-10-03 | Build site. |
| Rmd | cc84535 | brimittleman | 2019-10-03 | fix anno refseq |
| html | 7a9cf74 | brimittleman | 2019-09-24 | Build site. |
| Rmd | a2fe9d6 | brimittleman | 2019-09-24 | add annotation prep anaylsis |
I am putting together the necessary annotations
human fastq: /project2/gilad/briana/genome_anotation_data/hg38_try2 human anno: /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno gene 2 txn: /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno
/hg38_ncbiRefseq_txn2genename
For annotations:
Concatenate, change to gene names. I can use something similar to /project2/gilad/briana/genome_anotation_data/RefSeq_annotations/formatFullAnno.py
remove top line, Concatinate and sort:
#human
sed 1d hg38_ncbiRefseq_intron.dms > hg38_ncbiRefseq_intron.bed
cat *.bed > hg38_ncbiRefseq_Allannotation.bed
sort -k1,1 -k2,2n hg38_ncbiRefseq_Allannotation.bed > hg38_ncbiRefseq_Allannotation.sort.bed
python formathg38Anno.py
#results : /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno/hg38_ncbiRefseq_Formatted_Allannotation.sort.bedGenerate genome index for STAR
sbatch buildStarIndex.shLiftover the PAS from the first apaQTL project.
sed -e 's/^/chr/' /project2/gilad/briana/apaQTL/data/PAS/APAPAS_GeneLocAnno.5perc.sort.bed > ../data/liftover_files/APAPAS_withCHR_GeneLocAnno.5perc.sort.bed
sbatch liftPAS19to38.sh
#4 do not lift over
sbatch revLiftPAShg38to19.sh
#all reverse lift
sort -k1,1 -k2,2n ../data/liftover_files/APAPAS_GeneLocAnno.5perc.hg19lifted.bed > ../data/liftover_files/APAPAS_GeneLocAnno.5perc.hg19lifted.sorted.bed Full transcript annotations:
Download transcript bed file from online /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno/hg38_ncbiRefseq_transcripts.bed /project2/gilad/briana/genome_anotation_data/Chimp_refseqAnno/pantro6_ncbiRefseq_transcripts.bed
sort -k1,1 -k2,2n /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno/hg38_ncbiRefseq_transcripts.bed > /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno/hg38_ncbiRefseq_transcripts.sort.bed
sort -k1,1 -k2,2n /project2/gilad/briana/genome_anotation_data/Chimp_refseqAnno/pantro6_ncbiRefseq_transcripts.bed >/project2/gilad/briana/genome_anotation_data/Chimp_refseqAnno/pantro6_ncbiRefseq_transcripts.sort.bed
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.4.0 Rcpp_1.0.2 digest_0.6.18 rprojroot_1.3-2
[5] backports_1.1.2 git2r_0.25.2 magrittr_1.5 evaluate_0.12
[9] stringi_1.2.4 fs_1.3.1 whisker_0.3-2 rmarkdown_1.10
[13] tools_3.5.1 stringr_1.3.1 glue_1.3.0 yaml_2.2.0
[17] compiler_3.5.1 htmltools_0.3.6 knitr_1.20