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Old 04-16-2009, 11:57 PM   #5
Location: Toulouse

Join Date: Nov 2008
Posts: 21

We have run many, many cDNA projects on the 454 using GS 20, GS-FLX and now Titanium. The vast majority of these used SMART cDNA preparation, some with the Evrogen normalization, some without. We have had generally good results. Compared to genomic DNA sequencing cDNA sequencing generally produces fewer filter passed reads (more failures due to mixed reads) and the mean length is shorter. There is also more variability from library to library which probably is a DNA quality issue. I'd be happy to provide more information if you like.
we run only few project on our 454 (titanium only) and we were surprised about the amount of filtered reads and the length of the high quality reads. could you please tell me (if possible) the mean length and the percentage of passed filter?

For example, for our last run (4 regions, cDNA from chicken and duck), for 2 regions (chicken) we only have ~15% of passed filters (whereas Roche expects more than 50% for a titanium run - information from GSFLX Titanium metrics, but it may be for a genomic DNA project). Problems came from dots (cf attached spreadsheet).

Attached Files
File Type: pdf 09_04_03_filters_TCAG_summary.pdf (81.9 KB, 138 views)
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