Last updated: 2019-09-24

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Knit directory: Comparative_APA/analysis/

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/_STARtmp/

Untracked files:
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File Version Author Date Message
Rmd a2fe9d6 brimittleman 2019-09-24 add annotation prep anaylsis

I am putting together the necessary annotations for the snakefiles for the human and chimp data.

Chimp fastq: /project2/gilad/briana/genome_anotation_data/Chimp_genome chimp anno: /project2/gilad/briana/genome_anotation_data/Chimp_refseqAnno gene 2 txn: /project2/gilad/briana/genome_anotation_data/Chimp_refseqAnno/pantro6_ncbiRefseq_txn2genename

human fastq: /project2/gilad/briana/genome_anotation_data/hg38 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

#chimp
sed 1d pantro6_ncbiRefseq_downstream.dms > pantro6_ncbiRefseq_downstream.bed
cat *.bed > pantro6_ncbiRefseq_Allannotation.bed
sort -k1,1 -k2,2n pantro6_ncbiRefseq_Allannotation.bed > pantro6_ncbiRefseq_Allannotation.sort.bed
  
python formatpantro6Anno.py 
python formathg38Anno.py 

Generate genome index for STAR

sbatch buildStarIndex.sh

Liftover 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

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