csfastq analysis using Tophat 1.3.1
Hi! I was wondering - is there a way to load the .csfastq files downloaded from the SRA directly into Tophat 1.3.1, or can Tophat only handle separate .csfasta and .qual files?
Thanks in advance!
Thanks in advance!
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Hi,
tophat comes with a program called sra2solid which is supposed to prep the .csfastq file for use with tophat (trimming the quality score for the adapter, I think). I tried it and it seemed to work just as well as using separate csfasta & qual files. On the other hand, I didn't really get tophat to work to my satisfaction overall with the SRA SOLiD data set I was trying -- it didn't seem to find any splice junctions and I got a "malformed closure" error in one of the logs.
Good luck! -
I had the same problem with tophat for short SOLiD data (35bp). The current version of TopHat is optimized for reads more than 75 bp long. Have you tried other softwares and could you share your experience on that?Originally posted by thurisaz View PostComment
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Hi,
Sorry for not replying earlier -- I was away on holiday. I eventually used an older version of tophat (1.1.4) to align my SOLiD data.Comment
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Did you find junctions using that version? Does version 1.1.4 use seed-extend or split-align strategy? Thanks a lot.
Originally posted by thurisaz View PostComment
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