Hi,
I'm quite new in NGS. I'm looking for tools/stuff/idea to find DNA deletion. I'm working with illumina 100bp pair-end reads.
I have try to find lots of kind of tools/stuff on this forum to deal with DNA deletion.
I've tried using the classic pipeline Bowtie2/topHat2, but there are some ideas that disturbs me with this.
Indeed, tophat will seek to identify (donor sites / receiver) canonical splicing signals.
This is the strength of tophat for RNA-seq, but it does not interest me in my study.
On the other hand, Tophat gives me a outpout with an empty file deletion.bed for my candidate sample and full of things for my control sample...
In addition, I tried Pindel software, which is design to find deletion / indel / junction / etc, but again, this software is very limited for my analysis.
In fact, it only considers the reads themselves and not the size of the insert between the two mate of the same pair.
Finally, I used subread, but it manages only 16bp indel of maximum and DNA degradation/deletionI am looking for is quite large in size.
Currently, I am trying to perform an analysis with subjunc, which was developed to find the junctions, which in a sense could help me in my search for potential deletion.
Indeed, the first step to find the junction seems powerful, but the validation stage based on control of canonical splicing signals could be problematic.
So I look to the community if anyone can help me in my search for deletion.
thank you in advance
I'm quite new in NGS. I'm looking for tools/stuff/idea to find DNA deletion. I'm working with illumina 100bp pair-end reads.
I have try to find lots of kind of tools/stuff on this forum to deal with DNA deletion.
I've tried using the classic pipeline Bowtie2/topHat2, but there are some ideas that disturbs me with this.
Indeed, tophat will seek to identify (donor sites / receiver) canonical splicing signals.
This is the strength of tophat for RNA-seq, but it does not interest me in my study.
On the other hand, Tophat gives me a outpout with an empty file deletion.bed for my candidate sample and full of things for my control sample...
In addition, I tried Pindel software, which is design to find deletion / indel / junction / etc, but again, this software is very limited for my analysis.
In fact, it only considers the reads themselves and not the size of the insert between the two mate of the same pair.
Finally, I used subread, but it manages only 16bp indel of maximum and DNA degradation/deletionI am looking for is quite large in size.
Currently, I am trying to perform an analysis with subjunc, which was developed to find the junctions, which in a sense could help me in my search for potential deletion.
Indeed, the first step to find the junction seems powerful, but the validation stage based on control of canonical splicing signals could be problematic.
So I look to the community if anyone can help me in my search for deletion.
thank you in advance
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