Question: BAM detect unalign region
0
gravatar for muhammad.zarulhanifah
9 months ago by
muhammad.zarulhanifah0 wrote:

Hello folks,

I am running bowtie2 of a sequenced PCR product against a reference allele. Obviously here, my PCR product is bigger than the length of the sequence reads.

BAM containing unaligned region

How can I detect the presence of unaligned regions/positions early on without visualising on IGV?

Thank you.

bowtie2 • 104 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum131k • written 9 months ago by muhammad.zarulhanifah0
0
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:
samtools depth -r "chrom1:234-567" -a in.bam |\
awk '$3=="0" {printf("%s\t%d\t%s\n",$1,int($2)-1,$2);}' |\
sort -t $'\t' -k1,1 -k2,2n |\
bedtools merge
ADD COMMENTlink modified 9 months ago • written 9 months ago by Pierre Lindenbaum131k
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