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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository:https://github.com/estepi/ASpli
Confirm the following by editing each check…
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In the manual it says to do the mapping and then add the junctions ($rPGA junctions add /path/to/known_splice_junctions) . But, if I try to do the mapping before adding the gtf file I get the error:
…
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Dear Brian,
I am finding that fusion events are being repeated in separate rows, and are being incorrectly labeled.
For example, in the below excerpt from a star-fusion.fusion_candidates.final file,…
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Dear IsoSCM developers,
I've successfully run assembly command and what to compare differential 3'UTR usage in my dataset. When I run compare command I get the following traceback:
2015-05-27T12:07:…
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Dear Tim,
I have a big stranded RNA-seq data set from human (10 conditions and 50 samples). I want to use Vast-tools and diff for differential alternative splicing analysis and estimation of intron r…
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Hi Alex,
First, I just want to say thank you for all of your great work.
I am having trouble with the 2nd pass step, while including annotations on the fly, for Multi-sample mapping.
I believe anoth…
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Hi Daniel,
I just discovered a serious bug in the Arabidopsis run. Apparently the strand assigned to the junctions is sometimes incorrect. As an example, in At portcullis signals the f…
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I am getting the following error from JunctionSeq, which stems from issue with estimateDispersions (I believe). This output is after using the recommended parameter (method.dispFit = "local").
```
u…
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The exonerate parser in SearchIO fails when splice junctions interrupt codons.
Here is the failed command:
``` python
>>> g = SearchIO.parse('test.txt', 'exonerate-text')
>>> next(g)
Traceback (most…
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- Try getting total mismatches from flag rather than counting X cigarops