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Hey everyone,
I'm relatively new to RNAseq analysis and this site has been really helpful about it.
I've got a very specific question on alignment with Tophat2 and I can't seem to find an answer anywhere online.
I've got read files(in fastq format) which I aligned using Tophat2 and did some further analysis on. The fq files I have seem to have quality values which were generated with Illumina v1.5. I've read that the quality scores used in Illumina v1.5 are a bit different in encoding. Could this affected my alignments(and therefore the whole analysis)? Does TopHat2 make use of the quality scores while aligning and if so, is there any compatibility issue that can possibly affect my analysis?
I know it's late to think of it now but I've just read about the Illumina v1.5 difference in quality score encoding. I assume it should be ok, because I haven't had any errors while running Tophat2. but just wanted to make sure I'm not making a mistake here, omitting a crucial step or so.
I'm relatively new to RNAseq analysis and this site has been really helpful about it.
I've got a very specific question on alignment with Tophat2 and I can't seem to find an answer anywhere online.
I've got read files(in fastq format) which I aligned using Tophat2 and did some further analysis on. The fq files I have seem to have quality values which were generated with Illumina v1.5. I've read that the quality scores used in Illumina v1.5 are a bit different in encoding. Could this affected my alignments(and therefore the whole analysis)? Does TopHat2 make use of the quality scores while aligning and if so, is there any compatibility issue that can possibly affect my analysis?
I know it's late to think of it now but I've just read about the Illumina v1.5 difference in quality score encoding. I assume it should be ok, because I haven't had any errors while running Tophat2. but just wanted to make sure I'm not making a mistake here, omitting a crucial step or so.
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