Thread: subread
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Old 12-05-2011, 01:42 AM   #2
Wei Shi
Location: Australia

Join Date: Feb 2010
Posts: 235

Dear Hanshart,

Yes, subread can map junction reads. However it does this not by looking for the junction locations, but by using part of the read sequence to find the mapping location for the read. Therefore, the mapping location returned by subread for a junction is on one of the exons which are spliced with other exons (usually the one which has the largest segment in the read).

However, the subjunc program included in the subread package can find the precise junction location in the read and return a CIGAR string which gives the length of introns.

If you are using the latest version of Subread (1.1.0), you should be able to find a User Manual in the package which will give you a brief introduction to the algorithm used by subread.

Hope this helps.

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