I have a BED file which define an interval of 3'UTR. The example of my BED is like this:
7 127591299 127591705 ENSG00000004059 0 + 12 8940364 8941817 ENSG00000003056 0 - 11 64315966 64316738 ENSG00000173153 0 + 12 2803258 2805423 ENSG00000004478 0 +
The order is : Chromosome Start End Gene Name Length Strand
I need to extract sequence in aligned BAM with corresponding interval per gene name. Is there any tools to do that? Thank you.
I use samtool view to see specific sequence in the given interval. So, according to my BED file from the first line, I use this command :
samtools view 33_realigned.bam 7:127591429-127591705
And it gives subset of BAM (in SAM format) corresponds to that interval but not merged. Is it possible to get the merged sequence? Thank you
It looks like you are trying to make consensus sequence out of a bam file.