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Hello,
I ran the ribomap with the code:
ribomap-linux/scripts/run_ribomap.sh --rnaseq_fq SRR403882.fastq.gz --riboseq_fq SRR403888.fastq.gz --transcript_fa gencode.v25.pc_transcripts.fa --rnaUns…
misik updated
6 years ago
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$error
[1] "Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/"
[2] "At least 80% of man pages documenting exported objects must have run…
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Hi Brandon,
When running `create-rpbp-preprocessing-report` is there a way to pass `--ymax` for `plot-read-length-distribution`? It is fixed to fixed to 1.5e6 and in my cases most of reads are out…
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Add a config option named "keep_riboseq_multimappers". Its semantics are the same as "remove_rnaseq_multimappers", but in reverse. That is, if the key is present with any value, then riboseq multimapp…
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I rarely use deepTools for RNA-seq data, so apologies if that turns out to be a trivial issue.
I'm just wondering whether the documentation in regard to the RNA-seq handling should be improved.
Let's…
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From Zhengtao:
> I encounter an error when I run the example dataset following the instruction in https://github.com/dieterich-lab/rp-bp/blob/master/docs/running-example.md
>
> The command and e…
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```
`Traceback (most recent call last):
File "prune_transcripts.py", line 229, in
mm_df = workers.map(_find_mm_in_range, range(npart))
File "/usr/lib/python2.7/multiprocessing/pool.py", l…
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Hi Brandon,
I found something unexpected when plotted out metagene profiles using included IPy-notebook file "create-orf-type-metagene-profiles.ipynb" by using my own data from yeast.
Most of …
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Originally from @tmargus in Issue #34:
> create_orf_profiles.py can't pick up location of models. Where in configuration files these can be specified or program should figure out itself?
> Anyway,…
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- [x] Document "filtered" vs. files
- [x] Document using other BAM files