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Old 02-23-2012, 07:30 AM   #2
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Location: Upstate New York

Join Date: Sep 2009
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I assume you used newbler, and that you had about 370 thousand reads? Did you check the 454NewblerMetrics.txt file and/or the 454ReadStatus.txt file to determine how many reads the assembler thought it used? I would guess that the assembly was very fragmented so that many of the reads ended up in contigs that were too small to report. When doing transcriptome assemblies, Newbler has some rules about what gets reported as isotigs, contigs, or not reported at all --- don't remember them all off the top of my head.

Also, you did tell the assembler that this is a cdna assembly project, correct?
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