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I am trying to use the scasav1.0.1 docker in a Mac M1 system and I get the following error when running the test dataset. The main issue is that it says that it cannot read the input file right before…
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Hello
I tried using your program, but i keep getting the error
Traceback (most recent call last):
File "/home/pato/miniconda3/envs/vcf_anno/bin/vcf-annotator", line 393, in
annotator.ann…
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Directory ./ already exists. Writing into existing directory..
mkdir: cannot create directory ‘.//SCASA_testscasaHNVC02_20230414001259/’: File exists
Preparing for alignment..
Indexing reference.…
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### Description of the bug
Hi
I tried to skip all preprocessing qc steps using the following skipping options but I got a java null error on some path value:
**nf-params.json**:
```json
{
…
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Hi,
I'm looking at the and product of CAT, run only using TransMap and excluding the indel classification `r.extend(find_indels(tx, psl, aln_mode))`.
I'm now trying to build a table of orthologs…
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Hi,
From your paper, it said that you get the longest ORF using the gffread, but the output of stringtie does not have the CDS information. Could you please tell me how you get it?
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### Description of the bug
unzipping of fasta and gtf files fail, when I provide a relative path to those files. I can work around by either unzipping the file first, or by providing an absolute path…
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Hi Owen,
I am analyzing some targeted DamID samples for colleagues. We have 4 pairs of polII Fusion/DamOnly samples from drosophila and would like to compare the binding pattern between them on tar…
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Hi,
Thank you for the tool. I am using it for isoform quantification. As a test run I am testing it on one sample from 10xV2.
The command that I am using
`scasa --fastq ERX3806131/4861STDY74…
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Reading [common.avdl](https://github.com/ga4gh/schemas/blob/master/src/main/resources/avro/common.avdl#L8), I'm curious where the association between actual DNA sequences and segments is made. Why sho…