Hi,
I have multiple bam files in a folder, for example, there are two pairs (as marked in bold) with each file of pair being R1 and R2:
GC121284_ATCACGTT.220830.R1_trimmed.bam
GC121284_ATCACGTT.220830.R2_trimmed.bam
GC121284_TAGCTTGT.220830.R1_trimmed.bam
GC121284_TAGCTTGT.220830.R2_trimmed.bam
I am trying to write a bash script to identify the paired files (according to their barcode in bold) and merge them using samtools.
I would be grateful if someone could please suggest, how to write the script.
As said in my comment, it is on you to ensure that separate alignment of R1 and R2 is meaningful. Anyway:
# GNU parallel
ls *.R1_trimmed.bam \
| awk -F ".R1_trimmed.bam" '{print $1}' \
| parallel -j <njobs> "samtools merge -o {}_merged.bam {}.R1_trimmed.bam {}.R2_trimmed.bam"
# Loop
ls *.R1_trimmed.bam \
| awk -F ".R1_trimmed.bam" '{print $1}' \
| while read p; do samtools merge ${p}_merged.bam ${p}.R1_trimmed.bam ${p}.R2_trimmed.bam; done < /dev/stdin
You can condense it a bit if you are using GNU parallel.
parallel --dry-run --link -j <njobs> samtools merge -o {=1 s/.R1_trimmed.bam/_merged.bam/ =} {1} {2} ::: *.R1_* ::: *.R2_*
Thanks for the code. However, to me, it seems that the awk command is not functioning properly:
$ ls *.R1_trimmed.bam
GC121284_ATCACGTT.220330.R1_trimmed.bam GC121284_TAGCTTGT.220330.R1_trimmed.bam GC121284_TCCGTCTT.220330.R1_trimmed.bam
$ ls *.R1_trimmed.bam | awk -F ".R1_trimmed.bam" '{print $2}' >
$ ls *.R1_trimmed.bam | awk -F ".R1_trimmed.bam" '{print $2}' | parallel --dryrun -j 2 "samtools merge -o {}_merged.bam {}.R1_trimmed.bam {}.R2_trimmed.bam"
samtools merge -o ''_merged.bam ''.R1_trimmed.bam ''.R2_trimmed.bam
samtools merge -o ''_merged.bam ''.R1_trimmed.bam ''.R2_trimmed.bam
samtools merge -o ''_merged.bam ''.R1_trimmed.bam ''.R2_trimmed.bam
This too is giving a weird output file name which is causing an error:
$ parallel --dry-run --link -j 2 samtools merge -o {1= s/.R1_trimmed.bam/_merged.bam/ =} {1} {2} ::: .R1_ ::: .R2_
samtools merge -o {1= s/.R1_trimmed.bam/_merged.bam/ =} GC121284_ATCACGTT.220330.R1_trimmed.bam GC121284_ATCACGTT.220330.R2_trimmed.bam
samtools merge -o {1= s/.R1_trimmed.bam/_merged.bam/ =} GC121284_TAGCTTGT.220330.R1_trimmed.bam GC121284_TAGCTTGT.220330.R2_trimmed.bam
samtools merge -o {1= s/.R1_trimmed.bam/_merged.bam/ =} GC121284_TCCGTCTT.220330.R1_trimmed.bam GC121284_TCCGTCTT.220330.R2_trimmed.bam
I edited the code to fix it and confirmed it now works.
The output is still weird i.e. there are two extra (unwanted) outputs per merged file (in bold):
$ parallel --dry-run --link -j 2 samtools merge -o {=1 s/.R1_trimmed.bam/_merged.bam/ =} {1} {2} ::: .R1_ ::: .R2_
samtools merge -o GC121284_ATCACGTT.220330_merged.bam GC121284_ATCACGTT.220330.R1_trimmed.bam GC121284_ATCACGTT.220330.R2_trimmed.bam
samtools merge -o GC121284_ATCACGTT.220330_merged.bam_merged.bam GC121284_ATCACGTT.220330.R1_trimmed.bam_merged.bam GC121284_TAGCTTGT.220330.R2_trimmed.bam
samtools merge -o GC121284_ATCACGTT.220330_merged.bam_sorted.bam GC121284_ATCACGTT.220330.R1_trimmed.bam_sorted.bam GC121284_TCCGTCTT.220330.R2_trimmed.bam
samtools merge -o GC121284_TAGCTTGT.220330_merged.bam GC121284_TAGCTTGT.220330.R1_trimmed.bam GC121284_ATCACGTT.220330.R2_trimmed.bam
samtools merge -o GC121284_TAGCTTGT.220330_merged.bam_merged.bam GC121284_TAGCTTGT.220330.R1_trimmed.bam_merged.bam GC121284_TAGCTTGT.220330.R2_trimmed.bam
samtools merge -o GC121284_TAGCTTGT.220330_merged.bam_sorted.bam GC121284_TAGCTTGT.220330.R1_trimmed.bam_sorted.bam GC121284_TCCGTCTT.220330.R2_trimmed.bam
samtools merge -o GC121284_TCCGTCTT.220330_merged.bam GC121284_TCCGTCTT.220330.R1_trimmed.bam GC121284_ATCACGTT.220330.R2_trimmed.bam
samtools merge -o GC121284_TCCGTCTT.220330_merged.bam_merged.bam GC121284_TCCGTCTT.220330.R1_trimmed.bam_merged.bam GC121284_TAGCTTGT.220330.R2_trimmed.bam
samtools merge -o GC121284_TCCGTCTT.220330_merged.bam_sorted.bam GC121284_TCCGTCTT.220330.R1_trimmed.bam_sorted.bam GC121284_TCCGTCTT.220330.R2_trimmed.bam
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Before investing any effort, please confirm that separate alignment of paired-end data is indeed what you want and need.
These files are aligned files, I only need to merge these files like:
samtools merge -@ 8 -o GC121284_ATCACGTT_trimmed_merged.bam -n GC121284_ATCACGTT.220830.R1_trimmed.bam GC121284_ATCACGTT.220830.R2_trimmed.bam
But without writing the same script for every pair. Rather I am trying to write a script for samtools to identify the paired files (according to their barcode in bold) and merge them as separate file per barcode.