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Old 11-20-2009, 06:55 PM   #2
Location: Toronto

Join Date: Nov 2009
Posts: 24

Further breaking down reads as short as 32 or 36bp doesn't seem to be a sensible thing to me. I wouldn't use segments shorter than 25bp myself. Doesn't the default setting more or less work for you in your case? I used the -a 5 option with 32bp reads and things seem to work fine for me. To further increase sensitivity, you could supply known junctions via a GFF3 file or tune down the -F parameter.

BTW, I saw in your other post that you have worked with Burge's cerebellum data. Where did you get it? By following the accession numbers provided in their Nature paper, I get all but the cerebellum data of six individuals. Thanks!

-- Leo
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