View Single Post
Old 09-20-2012, 01:26 AM   #18
ZFHans
Member
 
Location: Leiden

Join Date: Jun 2009
Posts: 10
Default

Hi Shane,

At the moment I am trying to compare LSC vs. PacBioToCA, and if time and hardware permits SmrtPipe. I noticed that PacBioToCA reduces the dataset from 1 GB to around 400MB. Haven't checked error rate yet.
We have 30x coverage in short reads.
I am still struggling with LSC 0.2.1 This runs fine on a testset, but when it runs on the whole short read set (49 GB) I get an read error in awk (awk: read error (Bad address). It's not consistently on one point in the file. Sometimes this happens after processing 50MB, and once it reached 30 GB. I did different md5 checksums for the file and they are the same. Any suggestions are appreciated.

Thanks,

Hans Jansen
ZFHans is offline   Reply With Quote