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export PATH=/scratch/chadbren_root/chadbren99/ppxinyi/STAR-2.7.11b/bin/Linux_x86_64/:$PATH
which STAR
/scratch/chadbren_root/chadbren99/ppxinyi/STAR-2.7.11b/bin/Linux_x86_64/STAR
./download_refer…
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how can i make file like 'hg19.RefSeq.union.bed.gz', in my case, species is mmu/rno? thans
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Hello,
I'm trying to generate the files needed to extract the 3'UTR from the hg19 gene annotation (see below). The instructions above show how the `hg38_wholeGene_annotation.bed` file was generated…
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`ngd --taxids` seems to require `gimme_taxa.py` have the `-j`. Not sure if you want to update the documentation or one of the scripts?
```
$ gimme_taxa.py -o taxids.txt Hyphomicrobiales
$ ngd --d…
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Hello,
I have a refseq gff that contains two chromosomes in it which I wanted to use in the panaroo pipeline. I tried using the script to convert it to a prokka gff but I get only the second chromo…
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Download the glycan and protein datasets in preparation of pre-processing.
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Hi all,
I want to download a specific number (e.g., 1,000) of random--it's essential that they be random, although "representative" is perhaps a better word--RNA reference sequence transcripts, pre…
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Hi,
Following the assembly of various genomes, now I have to propose dedicated visualization tools.
I installed a Chado database, which is accessible with a dedicated user that I named Chado. I can …
akmg6 updated
3 years ago
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Hi:)
I ran kraken2.1.2 for my mice gut microbiome shotgun metagenomic analysis. I built a custom db by using the following command
```
kraken2-build --download-taxonomy --db refseq
kraken2-build …
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Hey, I am having some issues with fastmultigather and the scale of signatures:
Everything is in: `/group/ctbrowngrp2/scratch/annie/2023-sourmash-viruses`
I created protein sketches with the `cus…