Dear All,
I am not so sure about two Tophat settings. Please help.
1) "Number of mismatches allowed in the initial read mapping"
Based on the documantation, my understanding is: the reads are re-aligned to
transcriptome/genome if the mismatches in the initial alignment is more than
the set n
You're correct Jack. I've modified the Tophat wrapper to remove this
restriction; the change will make its way to our public server soon.
Best,
J.
On Feb 8, 2012, at 1:27 PM, Jack Colicchio wrote:
> In the new version of tophat they allow for over 3 mismatches in the initial
> alignment, howev
In the new version of tophat they allow for over 3 mismatches in the initial
alignment, however your server still gives an error if you attempt to move this
over 3. This is problematic for trying to map RNAseq reads where there is
moderate divergence between the RNA and the reference genome.
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