Hello Everyone,
Till now I have been writing simple scripts to do my work. Now I want to
automate my task.
I have no idea about submitting array jobs
So here is the explanation of what I want to do and then you can help me
how to design the script.
In a directory I have these 4 fastq files
A-122-3.XX.lane_1_P1_I24.sacCer3.sequence.fastq
A-122-3.XX.lane_1_P2_I24.sacCer3.sequence.fastq
A-2-3.XX.lane_1_P1_I47.sacCer3.sequence.fastq
A-2-3.XX.lane_1_P2_I47.sacCer3.sequence.fastq
I made this script to align my fastq files with yeast genome and it worked
perfectly fine
#!/bin/bash
for f in *_P1*
do
LB="${f%%.*}";
SM="${f%%.*}";
PU="${f%%.lane_*}";
PU="${PU#*.}";
NUM="${f%%_P*}";
NUM="${NUM##*_}";
ID="$LB-$PU-$NUM";
PART1="${f%%_P*}";
PART2="${f##*_P1_}";
qsub -l mf=30G -l num_proc=12 -cwd -V -j y -b y -N $LB
"/apps1/bwa/bwa-0.7.5a/bwa mem -t 12 -R
'@RG\tID:$ID\tPL:illumina\tPU:$PU\tLB:$LB\tSM:$SM' -v 1 -a -M
/cork/vgupta12/S.cerevisiae/indexes/bwa/sacCer3.fa "${PART1}_P1_${PART2}"
"${PART1}_P2_${PART2}" > ${LB}.sam"
done
Now the result I have is 2 .sam files namely A-122-3.sam and A-2-3.sam
This is what I want to do in the same script
*Convert all the sam files into bam files. Here is the command for one sam
file*
*samtools view -bS test.sam | samtools sort - test*
*Then make index files for all bam files. Command for one index bam file is*
*samtools index test.bam ##output is test.bam.bai*
I have further downstream analysis , but as of now I would like to get my
above script plus the commands I just mentioned above(highlighted part)
into one script only.
Any help would be appreciated.
Thanks for all the help so far
Regards
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