Aaron Graubert
Aaron Graubert
At least provide a `deactivate-global-python-argcomplete` script to take care of remaining cleanup tasks. I was surprised to find that after uninstalling, argcomplete was still lingering around and that I had...
You're absolutely correct. This seems to be a leftover counter from earlier in development. Thanks for pointing this out
The anaconda package is a legacy version of RNA-SeQC maintained by another group. The pip package rnaseqc, is a support module for aggregating data from RNA-SeQC. The best way to...
Would it be possible to provide the entire metrics file? This can be very helpful for diagnosing the issue. If not, could you at least show the count of `Total...
This seems to indicate that your data was a single-ended library. If that's the case, you need to run rnaseqc using the `--unpaired` flag. By default, several of the metrics...
Then something really bad happened during alignment. Rna-seqc is reporting 60 million unpaired reads out of your library of about 70 million reads. However, it doesn't include alternative alignments in...
That is certainly strange. Would it be possible to share some of the fastqs? Even just a subset of reads would help us understand what is going on.
Depending on access control requirements, you could upload them here if the data is safe to be shared 100% publicly, or you could upload them to a cloud storage platform...
No, in fact we require that the chromosome names in the gtf and bam match. Are you also observing a significant number of unpaired reads?
Can you provide the command used to generate these results?