Open GoogleCodeExporter opened 8 years ago
Sorry, it's my mistake.
Although the map.dat file was on the local hard disk but the MOSAIK_TMP
directory still pointed to the NAS.
Cheers,
Yao-Cheng
Original comment by yalin...@gmail.com
on 21 Jan 2011 at 1:28
Hi Yao-Cheng,
I was wondering the purpose you're using MosaikDupSnoop, since we may no longer
maintain it. In our next release, we'll let MosaikAligner outputting BAMs
directly, and only keep MosaikBuild, MosaikAligner, and MosaikJump.
Best,
Wan-Ping
Original comment by WanPing....@gmail.com
on 21 Jan 2011 at 9:28
Dear Wan-Ping,
I am trying to remove the duplicate reads from our poorly prepared mate-pair
library. I used to use the cdhit-454 or FASTX package to remove duplicate reads
then feed to MosaikAligner for more than a year. I just realized that
MosaikDupSnoop can do the trick and the idea of checking alignment position
(especially for paired-end) is much clever than blindly collapse identical
reads on either sides. However, the disk I/O is quite a problem especially most
of cluster nodes are attached to NAS or even virtualized.
A bit off topic, I am wandering how do people remove duplicate reads now (if
one takes the paired-end distance into account)?
Best regards,
Yao-Cheng
ps. Hope it's not cross posting.
Original comment by yalin...@gmail.com
on 22 Jan 2011 at 8:38
Original issue reported on code.google.com by
yalin...@gmail.com
on 20 Jan 2011 at 2:45