SEQanswers - View Single Post - Tophat: generate junctions.bed file from BAM file

pengchy · 07-09-2013, 07:47 PM

Hi Julien, very important information. Thank you.

I have the same needness, and find sam_juncs, component of tophat, can output the junction position information without depth and overhang.

The needness of a script to get junctions.bed from bam file produced by tophat is, from my point:
I want to subset the bam file by several different criteria and check the influence on the alternative splicing detection. This script will make the alignment unnecessary.

Thank you.

07-09-2013, 07:47 PM	#4
pengchy Senior Member Location: China Join Date: Feb 2009 Posts: 116	Hi Julien, very important information. Thank you. I have the same needness, and find sam_juncs, component of tophat, can output the junction position information without depth and overhang. The needness of a script to get junctions.bed from bam file produced by tophat is, from my point: I want to subset the bam file by several different criteria and check the influence on the alternative splicing detection. This script will make the alignment unnecessary. Thank you. Last edited by pengchy; 07-09-2013 at 07:58 PM. Reason: add information