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Currently UniProt isoforms resolve to a fairly technical SPARQL endpoint. Example: `uniprot.isoform:Q9H4X1-2` resolves to https://sparql.uniprot.org/sparql/?query=DESCRIBE%20%3chttp://purl.uniprot.org…
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Hi @andrewprzh , I am going through the read assignments file and looks like there are instances with multiple entries of same read ID, each entry has a different isoform listed althought it's the sam…
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Hello Liz,
Hope you are well. I was trying out the chaining on 11 of my samples, and the script ran successfully. However, I noticed some seemingly redundant transcripts that appear to be the same…
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Trinity returns a lot of isoforms in its output. How are these carried forward into the ultimate mega merge assembly?
For example, how would isoform 1 and 2 move forward through clustering steps? …
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Hello,
I am trying to generate a count matrix using abundance_estimates_to_matrix.pl script in Trinity, but I keep running into the same error.
/usr/lib/trinityrnaseq/util/abundance_estimates_to_m…
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Implement the `HeaviestBundle` algorithm described in Lee _et al._ (2003) to generate consensus sequences for a POA graph.
Can also be used to obtain RNA isoforms.
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**the exact command you tried to run**
Feel free to leave any original paths, we don't have access to your system
srun -N 1 -n 1 bash -c "flair collapse -g /home/mbauer/genome/gencode.43.GRCh38.prim…
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# Context
Should the[`feature_length`](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md#feature_length) requirements be updated per the conversation in [**#s…
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Some cell lines have multiple isoforms that are displayed in the gene editing tab:
![image](https://user-images.githubusercontent.com/25040762/120566665-907c3e80-c3c4-11eb-9596-c22796c3f195.png)
T…
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Hello,
currently, I am trying to run IsoformSwitchAnaylzer with Kallisto counts. After successfully using importIsoformExpression() to extract my count data, I wanted to set up the switchAnalyzeRlis…