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My first post to this forum... So please stay with me if I make some mistakes.
We did a SOLiD-run on HEK-293T cells transfected with a viral genome. We got around 300mil. reads from this. The reads are small, between 15 and 35 nucleotides because we trimmed of the p2 sequencing adapter before we used the TopHat pipeline.
Although the software works fine, we were expecting splice donor and acceptor sites flanking the aligned exons. We hardly see them in our results. It seems that the program just maps them at random! I thought that GT-AG rule was one of the key-rules of the program? This problem remains even at the standard-settings.
Another problem, it seems, is that there are still quite some errors in the seed-region even though we've put it on "0 mismatches" in the settings...
We played a bit around with the settings, but still both these problems remain... Does somebody have the same experience with this? Did someone do a succesfull analysis using TopHat on a SOLiD run with these small reads?
Any help would be welcome!
We did a SOLiD-run on HEK-293T cells transfected with a viral genome. We got around 300mil. reads from this. The reads are small, between 15 and 35 nucleotides because we trimmed of the p2 sequencing adapter before we used the TopHat pipeline.
Although the software works fine, we were expecting splice donor and acceptor sites flanking the aligned exons. We hardly see them in our results. It seems that the program just maps them at random! I thought that GT-AG rule was one of the key-rules of the program? This problem remains even at the standard-settings.
Another problem, it seems, is that there are still quite some errors in the seed-region even though we've put it on "0 mismatches" in the settings...
We played a bit around with the settings, but still both these problems remain... Does somebody have the same experience with this? Did someone do a succesfull analysis using TopHat on a SOLiD run with these small reads?
Any help would be welcome!