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The Docs specify that for fastq input files, gzip compressed files are accepted, but nothing is specified for the input reference fastas.
Does this mean coverm currently only accepts uncompressed fas…
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Hello,
I have an issue with the FASTA format. It is a FASTA format which was made from the Illumina Sequencing and annotated with KREGG. We have tried a first time wihtout Uniprot annotation and i…
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I am unable to get an index for any fasta I try. Here is below what I get if I try IKZF1 as a test:
```
out/wget/https/github.com/Oshlack/Toblerone/releases/download/v0.0.8/tinyt_amd64 index -i ou…
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Thank you for the great tool.
I am wondering if there is anyway to generate a Fasta based on the gene fusion output. I would like to quantify TPMs with Salmon/Kallisto which require a Fasta version…
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Hello
I've encountered a similar issue after running pyssw.py. May I ask how you managed to resolve it?
_Originally posted by @a30221274 in https://github.com/twopin/CAMP/issues/27…
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### Description of the bug
Perhaps fasta needs to be a "required" parameter, that is, perhaps the pipeline should fail immediately if the fasta paramenter isn't set to an (existing) fasta-file?
…
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Match [GDC](https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files)
- include decoys
- include viruses
Will need to
- [x] recreate reference files for all human (h38/hg19) ge…
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in case there is a merged input FASTA, use that one for the staging rather than the primary FASTA
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Hello, I am using the software in my non-model species data.
I want to ask how to obtain two files, training_mRNA.fasta and training_lncRNA.fasta, in this step. Is it a file that directly applies ex…
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Hi Jesse,
Thanks for your pipeline! I am still learning how to use it. I would like to use new released Silva 138.1 and PR2 5.0.0 for bbsplit step. I was wondering how did you create these files:
…