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For generating CAGE coverage files from bamcovergae. It will be good to allow generating 1 bp binned bam files where only 5' -most base-pairs are kept (keeping in mind the RNA-strand).
This is alread…
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It would be nice to be able to use bamCoverage meaningfully to look at ribosomal profiling. The new metagene options are largely doing that, but we need to add a modified version of the `--MNase` opti…
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While running the process-all-samples pipeline, STAR alignment completes successfully and creates the symlink as expected. However, the immediate steps thereafter can not recognize the bam file pointi…
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This behavior was originally discovered by @tmargus in Issue #35.
The setup.py script attempts to automatically grab misc and riboutils from the respective repos and install them using "pip3 instal…
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I think that it would be nice to have the "--minThreshold" and "--maxThreshold" arguments in plotHeatmap as well. computeMatrix with multiple samples can take quite a long time and being able to set t…
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computeMatrix ... --outFileNameMatrix test_matrix.tab gives this
Traceback (most recent call last):
File "/home/heyne/install/miniconda3/lib/python3.5/site-packages/numpy/lib/npyio.py", line 1158, …
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```
What steps will reproduce the problem?
1.-bash-4.1$ ngs.plot.r -G hg19 -R genebody -C
/srv/gsfs0/projects/cho/riboseq/bam/R10_R1.hg19.bam.bai -O R10.genebody
What is the expected output? What d…
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```
What steps will reproduce the problem?
1.-bash-4.1$ ngs.plot.r -G hg19 -R genebody -C
/srv/gsfs0/projects/cho/riboseq/bam/R10_R1.hg19.bam.bai -O R10.genebody
What is the expected output? What d…
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Here is the command + stack trace to repo
```
[gpratt@tscc-login1 ~]$ submit_miso_pipeline.py '--bam' '/home/gpratt/projects/roche_riboseq/analysis/npc_riboseq_v1/3R21_CAGATC_L008_R1.fastq.gz.polyAT…