Hi all, I need your guidance in this, I have dna sequence paired end reads with known non-reference transposable element sequence insertions (~1000 bp). I do have a reference genome. I am wondering if there are bioconductor packages, and/or other software that can help me identify the insertion sites. I would also like to pick your brains on how to go about doing this, what is the optimal protocol that is. Thanks a lot for your help, Al [[alternative HTML version deleted]]

Dear Alpesh, Not sure if this will help, but the Subread aligner in Rsubread package can detect ~200bp insertions. Cheers, Wei On Sep 9, 2014, at 3:13 PM, Alpesh Querer wrote: > Hi all, > > I need your guidance in this, I have dna sequence paired end reads with > known non-reference transposable element sequence insertions (~1000 bp). I > do have a reference genome. I am wondering if there are bioconductor > packages, and/or other software that can help me identify the insertion > sites. I would also like to pick your brains on how to go about doing this, > what is the optimal protocol that is. > > Thanks a lot for your help, > > Al > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}