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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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CircSkipJunctions does not contain junction orientation #48

Closed CDieterich closed 6 years ago

CDieterich commented 6 years ago

Here is another problem..

Linear Skip Junctions are reported as: 1:1257311-1273665:4

Unfortunately, it is not clear from this format if the junction is in Sense or antisense to the gene locus.

Please investigate

tjakobi commented 6 years ago

The strand information is available via temporary count files. Including the strand is straightforward by modifying the combine() function of CombineCounts.py. However, this will of course change the output format and may brake old downstream scripts.

CDieterich commented 6 years ago

Ok, we leave this for the next major release then (DCC 0.5)

tjakobi commented 6 years ago

Fixed by merging of 66c4d0373a2edfb19822c5bccb18255fb1151cba