Deconseq for paired-end data

[lili.fa...@gmail.com]

I have a question, my data is paired end sequences, but I couldn’t find paired-end option in deconseq manual.

As I read in bwa manual, “bwasw” accepts the mate file and performs paired-end alignment.

How about deconseq, can I use that for paired-end data? Is there any consideration while I am running the Deconseq for my paired-end data?How to write the command for the Deconseq for my paired-end data?

[Kate]

I don't know if Deconseq will handle paired end data.  But you can do it manually.  Just run deconseq on both files.  Then any reads that are removed from one file, you will need to remove the paired read from the other file.

[faizan saleem]

Dear Kate,

Can you please provide the script or link to resync the paired end files after the removal of contaminants as you have mentioned above?

Thank you.