Question: Tophat Settings
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Du, Jianguang • 380 wrote:
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 number (for example, the default
setting is 2). In other words, the re-aligning will continue until the
mismatches is equal to or below the set number. Is my understanding
correct? If I am right, I have one worry: will Tophat stop re-aligning
if the mismatch is below 2 (if I use the default setting). If it is
true, the read will not be aligned to where it belongs to (with 0
mismatch).
2) "Number of mismatches allowed in each segment alignment for reads
mapped independently"
Does this mean that the reads will be cut into segments if the
mismatches of alignment is more than the set number?
Thanks in advance.
Jianguang