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INDELS/JUNCTION Detection Paired End DNA SEQ
Hi everyone,
I am using paired end 100 bp reads on an illumina hiseq platform to find chromosomal rearrangements. I can find them just fine with the paired end data since the pairs are flagged, but I need to find the junctions within the sequence reads themselves. I've tried BWA, Bowtie2, Tophat2, SNAP, and ELAND and none of these report junctions except for Tophat2, but Tophat2 is not suitable since I'm sequencing DNA. I can see the junctions if I do not soft clip my reads, but it doesn't display the reads as junctions like it does when I use Tophat2 on RNA. Does anyone have any suggestions on how to get some of these programs to display split reads or filter them out into a separate file so I can find and analyze them effectively?
The junctions are also more than just a few base pairs. They can vary from a few KB to hundreds of KB and a few are inter chromosomal rearrangements.
I am using paired end 100 bp reads on an illumina hiseq platform to find chromosomal rearrangements. I can find them just fine with the paired end data since the pairs are flagged, but I need to find the junctions within the sequence reads themselves. I've tried BWA, Bowtie2, Tophat2, SNAP, and ELAND and none of these report junctions except for Tophat2, but Tophat2 is not suitable since I'm sequencing DNA. I can see the junctions if I do not soft clip my reads, but it doesn't display the reads as junctions like it does when I use Tophat2 on RNA. Does anyone have any suggestions on how to get some of these programs to display split reads or filter them out into a separate file so I can find and analyze them effectively?
The junctions are also more than just a few base pairs. They can vary from a few KB to hundreds of KB and a few are inter chromosomal rearrangements.
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