Mercurial > repos > chrisw > monorail_test
changeset 0:a25fa2b5e379 draft
Uploaded
author | chrisw |
---|---|
date | Tue, 12 Feb 2019 11:07:30 -0500 |
parents | |
children | 5c92c1163a6d |
files | monorail.sh |
diffstat | 1 files changed, 46 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monorail.sh Tue Feb 12 11:07:30 2019 -0500 @@ -0,0 +1,46 @@ +set -o pipefail -o errexit +#get this script's path +#p=`perl -e '@f=split("/","'$0'"); pop(@f); print "".join("/",@f)."\n";'` + +#/data7/miniconda2/envs/_galaxy_18.09/bin:/data7/miniconda2/condabin:/home/cwilks/.nimble/bin:/data/pypy3-v6.0.0-linux64/bin:/home/cwilks/zstd_dir:/data/bedtools2/bin:/usr/local/cuda-8.0/bin:/home/cwilks/Python3/bin:/data2/sqlite-autoconf-3110000.fts5:/data/java/bin:/data/ant/bin:/home/cwilks/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cwilks/samtools-1.2:/home/cwilks/samtools-1.2/htslib-1.2.1:/data/WiggleTools/bin:/data/kent_tools:/data2/liftover:/home/cwilks/bin + +path2=$PATH +#starp=`/bin/which STAR` +#stp=`/bin/which samtools` + +#e.g. /data7/references/ath10/star_idx +ref=$1 +#e.g. 4 +threads=$2 +#e.g. 10 +min_uniq_qual=$3 +#e.g. ./ath10/gtf/exons.bed +annotation=$4 +#e.g. ./tmp2 +tmp=$5 +#e.g. tmp/SRR8505407_SRP182756_ath10_sra_1.fastq.gz +reads1=$6 +#e.g. tmp/SRR8505407_SRP182756_ath10_sra_2.fastq.gz, just leave off if not paired +reads2=$7 + + +#racc=`perl -e '$r1="'${reads1}'"; @f=split(/\//,$r1); $r1=pop(@f); ($n1)=split(/[\._]/,$r1); print "$n1\n";'` + +#cd ${tmp} +#align +STAR --runMode alignReads --runThreadN $threads --genomeDir ${ref} --readFilesIn $reads1 $reads2 --readFilesCommand zcat --twopassMode None --outReadsUnmapped Fastx --outMultimapperOrder Random --outSAMreadID Number --readFilesType Fastx --outTmpDir ./star_tmp --outSAMtype BAM Unsorted --outSAMmode NoQS --outSAMattributes NH MD --chimOutType Junctions --chimOutJunctionFormat 1 --chimSegmentReadGapMax 3 --chimJunctionOverhangMin 12 --chimSegmentMin 12 > star.log 2>&1 + +sout="Aligned.out.bam" + +#sort +sorted_bam="sorted.bam" +samtools sort -T ./samtools_temp -@ $threads -m 64M -o $sorted_bam $sout > stools.log 2>&1 +#index +samtools index -@ $threads $sorted_bam >> stools.log 2>&1 + +#get coverage summaries +#bamcount $sorted_bam --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --lats bc > bc.log 2>&1 + +#echo $PATH > ${sorted_bam}.bai +#echo $starp >> ${sorted_bam}.bai +#echo $stp >> ${sorted_bam}.bai