How to Extract Specific Region on Bam file

0

I aligned all my Nanopore Rna-Seq reads with Human Reference Genome and Transcript (Then I had 2 different bam files one of them is aligned with Reference Genome other is aligned with Transcript)

I download reference files from:www.ncbi.nlm.nih.gov/genome/guide/human/

I want to extract chromosome X from the aligned BAM file. I tried extract region with samtools view command but it did not work I taken the error specifies an invalid region or unknown reference. Continue anyway.'

I used to check chromosome list with samtools view -H input.bam then the list for both bam file(transcript and genome)

@SQ SN:XR_928432.2 LN:810

Can you tell me what am I doing wrong ? and How to extract that region?


Nanopore


HG38


Rna-Seq


Genome

• 133 views

updated 29 minutes ago by

0

written 5 hours ago by

▴

30



Source link