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Hey guys, thanks for the tool! Very useful!
I'm a bit confused about the "num_reps" parameter. And also who it relates to the event probabilities.
I have implemented an alternative splicing (AS)…
ls233 updated
7 months ago
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Wizard (or cards) appears after the user clicks the Get Started button:
- [ ] Add three, stubbed out, simple, initial cards -- one for genes, one for enrichment, one for network
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Given a homozygous SNP / Indel, there shouldn't be a peptide detected that matches the canonical proteome at that location (given that all isoforms that can produce the canonical peptide have the vari…
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Good afternoon,
For my PAC-BIO sequencing I performed the 5' cap selection step. I recently found out that the Iso-Seq Tofu algorithm for collapsing is not appropriate for data that performed 5' cap…
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Hey I just stumbled upon your tool and paper. I read the README and saw you mentioned that:
"It operates on the cDNA of the longest isoformic protein-coding transcript of a gene"
Why is that? What …
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Have you loaded the SQANTI3.env conda environment?
- [X] I have loaded the SQANTI3.env conda environment
### …
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Hi,
I want to generate .gtf file containing information related to genes/isoforms which can be helpful to confirm data analysis by visualizing in genome browser with mapping (BAM) file. This will …
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Hi,
I wanted to make a request to add the --append-names flag in the call to rsem-calculate-expression:
--append-names
If gene_name/transcript_name is available, append it to the en…
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I am performing DIA-NN from FASTA digest library for Arabidopsis thaliana. I got FASTA file from [**_plants.ensembl_**](https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-58/fasta/arabidopsis_tha…
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Hi Yuanhua,
my code is as follows:
> brie-count -a genes.gff3 -S cell.bam -b barcodes.tsv.gz -o test2/ -p 15 -t any
this process ran for 15 hours, however, the result files don't contain the i…