I have a list of Refseq annotated gene coordinates and I would like to extract the reads for the same in one go. I have read many posts here and at Seqanswers, but those are restricted to a particular region. for example
samtools view input.bam "Chr10:18000-45500" > output.bam.
How can one do this for a list of genes with the Transcription start and end positions?
I tried doing this by extracting theit extr Refseq gene names and the associated coordinates from the genome browser at UCSC. Then using samtolls view input.BAM "mygenes.bed" > output.bam. But it extracts the reads and the format is not BAM.
I am new to NGS can someone help.