Hi
I have a couple of questions regarding RNA seq analysis. My questions are
1.I need to use a viral genome (very small, ~2kb ) as a reference genome
and it is not available in Galaxy. I guess I can use this data from my
history. I have a fasta file but I am not sure whether I have to do some
kind of indexing or not.
2. In Tophat, default for "maximum number of alignments to be allowed" is
40. What my understanding is a single read can be aligned maximum 40
different places. I am wondering why this is 40. Is there any specific
reason? If I need unique mapping, I have to use 1 instead of 40. Am I
correct?
Thanks
SP