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