Hi Everyone
I am interested in getting the junctions.bed file similar to the one we get when we run tophat but with different aligners like gsnap or bwa. Although tophat which uses bowtie as its aligner gives pretty much good results of junctions.bed file but it fails if the read length is small around 35 -40 bp. Even in the Tophat manual it says , for using tophat the read length should be 75bp and more.
Now gsnap deals pretty much well with short reads and it also says that it can find novel splice sites, but it does not give directly a junctions.bed file as one of its output as compared to tophat. Similarly is the case with other short read aligners.
So my question is there a way someone here on this forum has already dealt with to make a junctions.bed file by using gsnap or other aligners. I think i can write a perl script to make a junctions.bed file from sam file output of gsnap and other aligners.
Is there any other way to get junctions.bed file from these short read aligners.
Hope to hear from you soon
Regards
