Multiple alignements tophat
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3.0 years ago
Chironex ▴ 30

Hello everyone. I'M analyzing transposons and repetitive elements that are expressed in some tissues of cephalopods. First of all, I've aligned fastq paired end of rna of tissues to the genome of interest with tophat. Then I made counts of repetitive elements using output .bam align file produced by tophat. But....my doubt is: I read about a setting of tophat -g/--max-multihits <int> that allows up many alignements for read. I don't set hit when I started tophat. Do you suggest me to restart the analysis? What could be a paramenter to allow the detection of the biggest number of transposon?

alignment • 534 views
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That number is set by default to allow up to 20. If you expect more hits than that then you will have to re-map with a larger number.

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Okay, and I also have to set --report-secondary-alignments to see all the alignement produced, right?