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1 set -o pipefail -o errexit
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2 #get this script's path
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3 #p=`perl -e '@f=split("/","'$0'"); pop(@f); print "".join("/",@f)."\n";'`
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4
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5 #/data7/miniconda2/envs/_galaxy_18.09/bin:/data7/miniconda2/condabin:/home/cwilks/.nimble/bin:/data/pypy3-v6.0.0-linux64/bin:/home/cwilks/zstd_dir:/data/bedtools2/bin:/usr/local/cuda-8.0/bin:/home/cwilks/Python3/bin:/data2/sqlite-autoconf-3110000.fts5:/data/java/bin:/data/ant/bin:/home/cwilks/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cwilks/samtools-1.2:/home/cwilks/samtools-1.2/htslib-1.2.1:/data/WiggleTools/bin:/data/kent_tools:/data2/liftover:/home/cwilks/bin
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6
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7 path2=$PATH
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8 #starp=`/bin/which STAR`
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9 #stp=`/bin/which samtools`
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10
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11 #e.g. /data7/references/ath10/star_idx
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12 ref=$1
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13 #e.g. 4
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14 threads=$2
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15 #e.g. 10
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16 min_uniq_qual=$3
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17 #e.g. ./ath10/gtf/exons.bed
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18 annotation=$4
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19 #e.g. ./tmp2
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20 tmp=$5
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21 #e.g. tmp/SRR8505407_SRP182756_ath10_sra_1.fastq.gz
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22 reads1=$6
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23 #e.g. tmp/SRR8505407_SRP182756_ath10_sra_2.fastq.gz, just leave off if not paired
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24 reads2=$7
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25
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26
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27 #racc=`perl -e '$r1="'${reads1}'"; @f=split(/\//,$r1); $r1=pop(@f); ($n1)=split(/[\._]/,$r1); print "$n1\n";'`
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28
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29 #cd ${tmp}
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30 #align
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31 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
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32
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33 sout="Aligned.out.bam"
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34
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35 #sort
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36 sorted_bam="sorted.bam"
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37 samtools sort -T ./samtools_temp -@ $threads -m 64M -o $sorted_bam $sout > stools.log 2>&1
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38 #index
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39 samtools index -@ $threads $sorted_bam >> stools.log 2>&1
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40
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41 #get coverage summaries
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42 #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
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43
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44 #echo $PATH > ${sorted_bam}.bai
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45 #echo $starp >> ${sorted_bam}.bai
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46 #echo $stp >> ${sorted_bam}.bai
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