Hello,
Will TopHat work if R1.fastq and R2.fastq have their reads in different order?
What if R1.fastq has some reads whose R2 mate did not make it past QC, and viceversa (R2.fastq has some reads whose R1 mate did not make it past QC)?
I could only find this information about how it uses paired-end information after mapping independently each mate, but I can't find info on how it relates mate pairs to each other on the two files.
From: http://seqanswers.com/forums/showpos...49&postcount=2
Thanks for your input.
Will TopHat work if R1.fastq and R2.fastq have their reads in different order?
What if R1.fastq has some reads whose R2 mate did not make it past QC, and viceversa (R2.fastq has some reads whose R1 mate did not make it past QC)?
I could only find this information about how it uses paired-end information after mapping independently each mate, but I can't find info on how it relates mate pairs to each other on the two files.
TopHat maps left and right reads separately using Bowtie, that is, it doesn't use Bowtie's pair searching like --fr, --rf, --ff. Using the mapped reads, TopHat finds pairs if the two reads of a pair are on different strand (it ignores if they are on the same strand) and the inner distance is within user specified range.
Thanks for your input.
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