-
Sometimes an isoform version of the canonical gene ID is used to annotate a causal pathway model. We should update the GO-CAM API's `getGPModelsWith2CausalMFs` SPARQL [query](https://github.com/geneon…
-
Added terms for creatine kinase MM, BB, MB isoforms-- all of them should have LOINC terms.
-
1. Run build-sbt.py with parameters suggested in #8
- takes list of samples, raw reads
- each leaf in tree are kmers in whole sample
- output to disk as .json tree structure, false positive rates (hi…
-
### Name of the tool
cuffnorm
### Tool homepage
http://cole-trapnell-lab.github.io/cufflinks/
### Tool description
normalize the expression levels from a set of RNA-Seq libraries.
### Tool outpu…
-
Hello,
I recently started to use ASpli to quantify the alternative splicing levels of my gene. My gene has 3 isoforms which only differ from each other by one exon.
- The first one has all exons…
-
Hello,
I could use your help troubleshooting this! Thank you so much!
****THE COMMAND I RAN FOR QC:****
`sqanti3_qc.py m64345e_220712_195752.gff genes.gtf GCA_000001405.15_GRCh38_no_alt_analys…
ghost updated
4 months ago
-
Comet supports a joint search for two enzymes and we have seen first interesting datasets
where this was used.
Should be relatively easy to implement and add a lot to flexibility. Great for making d…
-
[update]: oops, I just realized you can use `kallisto quant-tcc` to do this
I know there are workarounds for this but it would be nice to have a `--transcript-counts` option for `bustools count` th…
-
Hi, I aligned the transcript to the reference genome, and based on the coverage of reads, I found two alternative splicing events. However, the GTF file expanded by IsoQuant shows only one transcript …
-
- [x] fix excessive # of genes
- [x] fix out of order isoforms
- [ ] fix bad gene count (1400, should be 42K)
---
From apollo-performance code
```
grep "WormBase\tgene\t" loaded-data/worm/…