Skip to first unread message
chil...@gmail.com
May 30, 2017, 10:15:00 PM5/30/17
to Edwards Lab Tools
Hi, DeconSeq group
I am using the DeconSeq(deconseq-standalone-0.4.3) for mouse host reads remove and have one questions about paired-end sequence data.
I merged my two paired-end read files into one file by ‘cat‘ command simply, and ran the Deconseq using the merged file as the input file. The final output file *_clean.fq includes reads and their mate reads, no orphaned reads are found.
Does the software use pair-end information? If do, how does it filter contaminant reads of paired-end data? For clean reads, both the read and mate read are need to be unmapped against host genome? Or just either of paired-end reads is unmapped?
Regards,
JY
I am using the DeconSeq(deconseq-standalone-0.4.3) for mouse host reads remove and have one questions about paired-end sequence data.
I merged my two paired-end read files into one file by ‘cat‘ command simply, and ran the Deconseq using the merged file as the input file. The final output file *_clean.fq includes reads and their mate reads, no orphaned reads are found.
Does the software use pair-end information? If do, how does it filter contaminant reads of paired-end data? For clean reads, both the read and mate read are need to be unmapped against host genome? Or just either of paired-end reads is unmapped?
Regards,
JY
Reply all
Reply to author
Forward
0 new messages