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### Use Cases
1. As a user of the Platform, I would like to see the types of orthologues and paralogues that have been identified for my target of interest.
### Summary Views
![gene_tree_summ…
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I build a Pseudomonas database according to the codes on the website. After cd-hit completes, I don't get *.bak.clstr file. And after makebalstdb completes, I only get three .p* files, that is .phr, .…
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Currently as far as I see regexes here are only for Unicode text. But they can be used to parse binary files as well (to to parse a mixture of binary and text).
For example, how can one implement `st…
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Hi, I got some issue on 'add_log2_depth' during running CNVkit on PoN.
It seems like the problem is that "add_log2_depth" receive a set of depth values as a string instead of one-by-one.
Here is…
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from
https://github.com/geneontology/go-annotation/issues/1873#issuecomment-385926637
- [x] tra2 NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2 kinase activity GO_Central …
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My team encountered a couple of problems and unclear concepts during our work and we would like feedback to help us understanding better.
1. INDRA statements: we could not find information on how d…
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Hi everyone,
The OrthoFinder run I was performing encountered an error at the species tree inference step.
The only logged error message was:
`ERROR: An error occurred`
`ERROR: Species tree in…
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I have received an error trying to find tandem duplication using jcvi.
hemzy@DESKTOP-J3FNUQU:~/MCScan/ATHALY/ATHATHtandem$ python -m jcvi.compara.catalog tandem ATHp.blast ATH.cds ATH.bed -o ATH.ta…
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Hi,
I am running stringtie with gencode v22 annotation on one of my samples of human RNA-Seq data from a cell line.
The command I am using:
stringtie JH_04.sorted.bam -G Gencode.v22.annotation.gtf -…
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For paired-end alignments generated with STAR, the reported ExonReads number is almost exactly double the number that STAR generates using the --quantMode GeneCounts option. Counts generated using ka…