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Old 06-06-2014, 12:43 PM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default Bam file to junctions.bed


I received aligned BAM file and do not have a raw sequence file.

My aim is to count how many reads skip exon 7 of a gene and how many reads do not skip, in addition to reads that span exons 6 and 7 ; 7 and 8.

Ex 6-------- Ex 7 -------- Ex 8
___________ __________ => Condition1: reads that span 6-7 and exs 7-8
____//////////////////////___ => Condition 2:reads skipping exon 7
___________________ => Condition 3: reads that span exon 6,7 and end in 8.

Is there a way to get numbers from my BAM file for above 3 conditions.

Yes, if I have raw reads, i would use TopHat and get junctions.bed to deduce these. However, the BAM file was not generated using TopHat and I don't have access to raw sequences.

Is there a way to get junctions.bed - perhaps convert bam to FASTA and then realign using Tophat. This potentially 'would' corrupt the paired end structure..leading to loss of read numbers..( I am not so sure about this though)


Is there any other smart way to just count reads that jump exon 7.

Appreciate any response. Thanks a lot.

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