I have some fastq files that contain a sequence length distribution that are not uniform. Most sequences are trimmed at 75bp with ~3/8ths at 74bp ~1/4th at 73bp and trailing off all the way to the 34bp length. This closely resembles an exponential curve. Anyway, I am curious if the varying lengths will cause problems when attempting to use TopHat2 to align to a reference genome.
2 answers
Tophat2 supports variable read-length. So using Tophat2 won't be an issue. Personally, I don't use reads with length less than 40 nt. I don't think reads with variable read lengths will cause any problem with the interpretation of results generated from Topaht2.
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written
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Ashutosh Pandey
That'll be fine. Variable lengths are pretty much the norm post-QC.
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