QuasR - importing alignment files from other aligners
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@svenschuierer-7087
Last seen 4.4 years ago
Switzerland

I was wondering whether it is possible to import alignment files from other aligners into quasR (e.g. STAR or Tophat2) in order, for instance, to run qCount on them.

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@hotz-hans-rudolf-3951
Last seen 4 months ago
Switzerland

Hi Sven

 

Yes, this is possible, as long as the alignemnts are stored as bam files. Have a look at the vignette (section 5.1
"Create a sample file"), where the three supported input files are described. In short: You create a sample file listing the bam files instead of the fasta/fastq files. Obviously, you will loose some functionality of QuasR.

 

Hope this helps, Hans-Rudolf

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