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Old 07-31-2009, 09:33 AM   #35
Location: Texas

Join Date: May 2009
Posts: 32

Hi, I have been testing the trial version of CLC workbench and I encountered two issues.

1. I BLASTed a set of illumina generated short reads (17-33, after trimming the 3'adapters) to mouse RefSeq database through stand alone BLAST program with stringent parameters and I found, say 2500 reads matching to mouse mRNAs. When I aligned all those 2500 reads to the same RefSeq database by using CLC reference assembly, only half of them are aligning to the reference. I tried all different options available changing the gap penalties, global alignment, scores etc...but never all the reads aligned to the reference. I think there should be more options here.

2. I used BLAST feature in CLC bench and when I view the blast output parsed results, I dont see all the columns in the overview table. For example I dont see strand orientation titled column in the overview. However, I see it in the individual blast mapping, but it is useless for me because I need to count the total number of minus and plus mappings of the total number of mappings. This is a serious limitation for me.
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