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Hi!
I'm doing a project to do Differential gene expression on non-coding RNAs, so was planning to filter counts file only for non-coding probability.
But for that to happen, I'd need the read i…
idlip updated
3 weeks ago
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Picard and HTseq are still in a conda environment that must be activated when starting the script
We have found no docker images with functional Picard
For HTseq, we should create a docker image c…
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We are already using this in another project. PyVCF is nicely written and very fast.
Library repo
https://github.com/jamescasbon/PyVCF
Documentation
https://pyvcf.readthedocs.io/en/latest/
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When one or more BAM check fails within the group, htseq-count of the entire group fails. Any way to implement an option so that one can htseq-count on the remaining passing BAMs in the group?
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I am trying this tool, part till alignment ran fine but at htseq count step found the following error
/usr/bin/python2.7 htseq.script.count not found.
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There was quite a few differences identified by looking at the barplots between kallisto's mapping (based on TPM data) and HTSEq mapping (based on Tophat2/HTseq). See the folder PredictorsDietInduced…
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**Tracking ticket** Once the problem is resolved and Main updated (as needed) we can close this out.
**Workaround** Use HISAT2 instead of RNA STAR.
**Example error**
```
Fatal error: Unknown e…
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First of all thank you so much for your wonderful tool and for the STAR GeneCounts module you already implemented! It works just great! However it would be great if you could make the Assigned reads (…
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```
pysam/libchtslib.c: In function '__Pyx_PyCFunction_FastCall':
pysam/libchtslib.c:15077:12: error: too many arguments to function '(PyObject * (*)(PyObject *, PyObject * const*, Py_ssize_…
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I am still in the process of updating Trinity around here, natively in our install, including more _and_ less things than what you put into the container (which is quite an eclectic bunch of packages,…
drhpc updated
2 years ago