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:https://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?