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The YAML and submissuib command are attached.
[prepare-alternative-expressed-tx.sh.txt](https://github.com/dieterich-lab/rp-bp/files/942475/prepare-alternative-expressed-tx.sh.txt)
[alternative.ya…
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From @tmargus, first mentioned in Issue #34
> It runs up to STAR alignment and finished with empty BAM files.
> I found that reason was input method for STAR. It assumes input fastQ to be compres…
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when I try to run example, here comes an error during ORF prediction step.
I ues command:
`run-all-rpbp-instances c-elegans-test.yaml --overwrite --num-cpus 2 --logging-level INFO --keep-intermedi…
PSSUN updated
6 years ago
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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/JokingHero/ORFik
Confirm the following by editing…
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This is directly connected to dieterich-lab/rp-bp#59. Any fix there will need to involve `ribo_filenames`.
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Several scripts use deprecated versions of pandas helpers. They should use the versions in `misc.pandas_utils` rather than `misc.utils`.
- [ ] `extract-orf-coordinates`
- [ ] `label-orfs`
- [ ] `…
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On Lines 44, 45 of prepare-rpbp-genome, the name of the exons file for the transcript isoforms is:
```
exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name']…
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Hi Joshua,
Thanks for helping with my previous post re: mapfactories not working. Your workaround was great. This is less of an 'issue' and hopefully more of a discussion.
My main question is wh…
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I open this thread to follow-up on minor issues related to the analysis scripts, when running the example dataset (see also #76 ).
1. When running `create-rpbp-preprocessing-report`, call to pdfla…
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From Charlie:
> I am having trouble running it on my data (human genome, refSeq genes in GTF annotation, de novo genes in GTF annotation, ensemble rRNA). I've confirmed in IGV that the GTFs look ap…