Browsing mappings for multiple BAM files
Hi all,
Thanks to helps of Biostars community, I managed to map SOLiD RNA-seq reads to a macaque genome assembly (macFas5). Now, I have 251 bam and bam.bai files to look into. I want to see whether there are any reads that map to a certain region on chromosome 11 and I have to do it for all bam files I have. So, I was wondering if there is a more practical way to check this than zooming into the same region in each bam file using IGV.
Thanks in advance.
2 answers
find DIR1 DIR2 -type f -name "*.bam" | while read B; do echo -n "${B} " && samtools view -c ${B} "chr11:456-789" ; done
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Pierre Lindenbaum
You can use bedtools' multicov https://bedtools.readthedocs.io/en/latest/content/tools/multicov.html to do this pretty easily
bedtools multicov
Ensure that all your bam files are sorted and indexed.
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You can extract the mapped reads on a given region using samtools : Extract Reads From A Bam File That Fall Within A Given Region