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8.1 years ago
manman
•
0
Using Galaxy's Orione pipeline Illumina paired end sequences were trimmed using both the positional trim and the sliding window trim. These were then subjected to de novo assembly using velvet and SPAdes. With both assemblers the sliding window trimmed data failed to assemble. Is anyone aware of any issues regarding this or why these issues may be arising? Is this an issue isolated to Orione?
Did you look at the stats (FastQC) of the trimmed files? Perhaps reads were trimmed to an extent where they have become too short to be useful for assembly. You will need to reconsider your choice of trim options in that case.
Did the untrimmed data assemble BTW?
Yes, both the untrimmed and the data trimmed with the positional trim assembled. Unfortunately I can't access the FastQC files for it at the moment because the Orione server is down. Thanks for the help.