Hi,
I found several novel transcripts using RNA-Seq data (paired-end reads), in intergenic regions. Some of them have 2 or 3 exons.
Now I have:
1) a BED file with chromosome location of entire transcripts (from the first base of first exon to the last base of the last exon)
2) a BAM file with the reads, mapped in these regions.
So, my question is:
How can I extract the exact chromosome location (BED format) of single exons for each novel transcripts?
I mean, is there any solution using well known tools?
Thanks a lot,
Mattia.
I found several novel transcripts using RNA-Seq data (paired-end reads), in intergenic regions. Some of them have 2 or 3 exons.
Now I have:
1) a BED file with chromosome location of entire transcripts (from the first base of first exon to the last base of the last exon)
2) a BAM file with the reads, mapped in these regions.
So, my question is:
How can I extract the exact chromosome location (BED format) of single exons for each novel transcripts?
I mean, is there any solution using well known tools?
Thanks a lot,
Mattia.