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Have Mikado pick realise that "reference" transcripts should not be summarily excluded #148

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lucventurini opened this issue Feb 13, 2019 · 0 comments
Closed

Have Mikado pick realise that "reference" transcripts should not be summarily excluded #148

lucventurini opened this issue Feb 13, 2019 · 0 comments
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Version 2
Milestone
2.0

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@lucventurini
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Currently, "reference" transcripts are passed-through by Mikado prepare, but their special status is ignored from that point onwards.

Fixing this issue requires Mikado to:

a- mark clearly reference transcripts in the "prepared" GTF
b- ignore the "requirements" check during Mikado pick.
@lucventurini lucventurini added this to the 1.5 milestone Feb 13, 2019
lucventurini added a commit that referenced this issue Feb 13, 2019
@lucventurini
Commit potentially solving #148
9637ffd
lucventurini added a commit that referenced this issue Feb 13, 2019
@lucventurini
Fixed a small bug for #148
7d24c82
lucventurini added a commit that referenced this issue Feb 13, 2019
@lucventurini
Additional provision for #148: do not exclude as fragments loci that …
48f6406 
…have reference transcripts.
lucventurini added a commit that referenced this issue Feb 13, 2019
@lucventurini
Hopefully fixing the Travis errors. Also, additional functionality for …
6a55708 
…#148: discarding any locus with no reference transcript in the "update" mode.
lucventurini added a commit that referenced this issue Feb 13, 2019
@lucventurini
Fixed a very small bug for #148.
b2a82ab
lucventurini added a commit that referenced this issue Feb 15, 2019
@lucventurini
Solved a bug for #148
7f8e2fa
@lucventurini lucventurini reopened this Feb 19, 2019
lucventurini added a commit that referenced this issue Feb 21, 2019
@lucventurini
This commit fixes a major bug introduced by a type-change of the Netw…
7f42ba6 
…orkX "neighbors" method of graph objects. Nominally found thanks to #148
@lucventurini lucventurini added this to Closed in Version 2 Oct 15, 2020
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Commit potentially solving EI-CoreBioinformatics#148
5ac4763
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Fixed a small bug for EI-CoreBioinformatics#148
08947fa
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Additional provision for EI-CoreBioinformatics#148: do not exclude as…
b0708e1 
… fragments loci that have reference transcripts.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Hopefully fixing the Travis errors. Also, additional functionality for …
13b2533 
…EI-CoreBioinformatics#148: discarding any locus with no reference transcript in the "update" mode.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Fixed a very small bug for EI-CoreBioinformatics#148.
7fb021c
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Solved a bug for EI-CoreBioinformatics#148
2badb57
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Fixed EI-CoreBioinformatics#148; also, now metrics/score files will c…
d37f8a5 
…orrectly report whether a transcript was "reference" to begin with.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
This commit fixes a major bug introduced by a type-change of the Netw…
885038b 
…orkX "neighbors" method of graph objects. Nominally found thanks to EI-CoreBioinformatics#148
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