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@kelly-sovacool can you create the reference files for:
Fasta: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/100/555/GCF_011100555.1_mCalJa1.2.pat.X/GCF_011100555.1_mCalJa1.2.pat.X_genomic.fna.gz…
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Hi,
I was wondering if I would like to calculate coverage across the genome for specific window size (ex. 100kb) using a BAM file, do I need to supply a reference genome file when I run PathDepth? Or…
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Download reads from [Sequence Read Archive (SRA)](https://www.ncbi.nlm.nih.gov/sra) for an organism with a good reference. If that has a high SNP count then it is a pipeline issue.
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Can I use NCBI to construct a reference genome?
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I have created the whole genome bacterium reference list. How many reference genomes can be genome reference lists?
Can 9,000 reference genomes apply?
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Hi there, thanks for this awesome package! Fills our needs almost perfectly, and I'm excited to use it. My species of interest has a reference genome, but unfortunately it's of the heterogametic sex. …
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Is there any way to use reference genomes of organisms other than hg19, hg38, mm9, and mm10?
I am trying to use facets for dog samples (canFam3) and the first part of generating pileup file works …
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Hi, authors!
The pipeline is very good! I ran it successfully. But why the transcript's start and end position of reference species in the final chain file is different from its annotation file (gt…
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Expected Behavior
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For Bugs:
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### Environment
#### Steps to Reproduce
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Hi，I see you only provide mm10&hg19 reference genome build. if I want to use HiCorr on other species, would that do? are there any special requirements for the reference genome build?