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helper script to map features to genomic regions as BED files (code exists)
Add all mentioned helper scripts to the respective recipes and link from the main repository to the recipe so it’s always i…
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Hello,
Thank you for developing the tool.
If I am expecting a repeat may or may not start with the `--regions regions.bed`, but will extend beyond the genomic regions that are defined within `--…
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I find it useful to see the absolute genomic coordinates when working with large chucks of DNA and even with genes, for instance, when working in parallel with other tools such as genome browsers or B…
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## Feature request
### Tool(s) or class(es) involved
This is a request for a new tool
`GencodeRegionsAsBED`
### Description
Given a GENCODE gtf, create a BED file with the region of the genes…
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Thanks for developing so helpful tool !
I was trying to quantify signal at transposable elements from Pol2 ChIPseq and ATAC-seq.
I guess that TElocal can do this. However, I only used TElocal on R…
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Thank you for the great utility. Muse call in version 1 supported specifying genomic regions of interest via a bed file. (option -l). Am I correct this has been removed in version 2? Is there any way…
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Hello,
thanks for developing and maintaining this fascinating project.
I am trying to reproduce some of data pre-processing steps and couldn't figure out how exactly un-mappable genomic regions ar…
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Hello I'm trying to create the standard Kraken 2 database, with the following command:
kraken2-build --standard --threads 16 --db kraken-Sdb
I'm getting this:
Step 1/2: Performing rsync file …
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Good day,
I would like to perform Differential methylation scoring.
Is there a way to identify the number of hypo and/or hyper differentially methylated regions in introns, exons, promoters, TSS, 5′…
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Hi everyone I am new to MaSuRCA Reference guided assembly. I am using chromosome_scaffolder.sh for scaffoding. I have shared the log info, I don't know what is the error. Could you help me with this?
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