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**Describe the bug**
Hello, I'm trying to run SCENIC+ using SnakeMake in a linux machine (centos 9), on the tutorial dataset.
I ran scATAC-seq preprocessing in python (using pycistopic, using the tu…
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### Description of feature
Currently testing TreeVal by running daSamNigr - the European elder.
The peptide subworkflow, is obviously slower however does not **require** any futher optimizations.
…
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Hello, I am new to DROP. We have a single affected sample and hence wanted to use the publicly available control dataset of external counts. First I wanted to test the pipeline to see if I have setup …
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Hi,
I'm trying to generate a library from scratch based on GRCh38 with some regions masked (GRC exclusions). Very early in the main script, the reference genome FASTA is copied to a file with the m…
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Hi there,
I've been running some annotation tests on DFAST for a collection of MAGs and I noticed that in some cases, the a huge number of partial pseudogenes being detected, sometimes close to 20% o…
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### Description of feature
Prompted by the strategy presented in https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1 it would be an interesting general strategy to add a post-profiling step t…
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### Description of feature
https://github.com/nf-core/genomeannotator/tree/dev/modules/local/augustus
Secondary option for eukaryote genome mode (low priority to implement)
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I’m looking for gene prediction alternatives to MetaEuk that are less resource intensive for my VEBA software suite (https://github.com/jolespin/veba). With a cursory glance at the repo, it looks lik…
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Is there a way to pass in a non-custom genome build in the read_coldata() step ?
My reads are aligned to a specific mouse strain genome but it is not the standard mm build.
Thanks.
jcm6t updated
4 months ago
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Hi, thanks for creating this amazing tool!
I have 90 nearly complete MAGs, and I'm looking to identify amino acid auxotrophy using GapMind. Since the web version is challenging to use with so many g…