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Automatically exported from code.google.com/p/assemblyline
Unstranded transfrags in intronic regions should be assigned strand
corresponding to the intron orientation unless higher priority information is
available from strand-specific libraries
Otherwise unstranded transfrags will not get culled out using the intron
filters.
Potentially could mark intronic transcripts during initial parsing.
Original issue reported on code.google.com by [email protected]
on 26 Mar 2013 at 7:52
Using poly-A site lists will improve definition of transcript ends and enable
transcripts to be split correctly
1. Discover poly-A sites using RNA-Seq, ChIP-Seq, etc
2. Add to known DB of poly-A sites
3. Incorporate poly-A DB into assembly step
Original issue reported on code.google.com by [email protected]
on 9 Dec 2011 at 5:11
For each intron maintain scores
Makes it easier to filter intronic transfrags
use interval trees do intersect intronic transfrags with introns and find
highest scoring overlapping intron to use for filter
Original issue reported on code.google.com by [email protected]
on 26 Mar 2013 at 7:54
Study and improve least-squares smoothing algorithm for node densities
Original issue reported on code.google.com by [email protected]
on 9 Dec 2011 at 5:13
Use expression signal rather than number of transcripts when computing prior
weights
Original issue reported on code.google.com by [email protected]
on 27 Mar 2013 at 2:52
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