Hey folks-
I wasn't sure about which forum to post in. I would like to know if anyone has done or has advice in how to align reads to transposons in the genome?
I'm would like to do this in C.elegans, but the idea is consistent with any organism that encodes transposons. The sequence of the full transposon (inverted seq + transposase) has been a previously identified. However, I would like to also map the sequencing reads to transposons remnants that may only have the inverted sequences.
A technical hurdle is that the potential target sequences could be as short as 54bp and they are often repetitive.
An idea is to use a motif finder among the reads. I haven't done this before, but could this method circumvent aligning to the genome by just searching through all the reads? Does this method sound feasible to anyone that has used motif finders? Suggestions for platform/program is welcomed.
I'm really a novice in deep sequencing and the bioinformatics. I do have access to the CLC-BIO platform and I think I can learn some command line too...
Thanks for your time!
I wasn't sure about which forum to post in. I would like to know if anyone has done or has advice in how to align reads to transposons in the genome?
I'm would like to do this in C.elegans, but the idea is consistent with any organism that encodes transposons. The sequence of the full transposon (inverted seq + transposase) has been a previously identified. However, I would like to also map the sequencing reads to transposons remnants that may only have the inverted sequences.
A technical hurdle is that the potential target sequences could be as short as 54bp and they are often repetitive.
An idea is to use a motif finder among the reads. I haven't done this before, but could this method circumvent aligning to the genome by just searching through all the reads? Does this method sound feasible to anyone that has used motif finders? Suggestions for platform/program is welcomed.
I'm really a novice in deep sequencing and the bioinformatics. I do have access to the CLC-BIO platform and I think I can learn some command line too...
Thanks for your time!