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We have encountered an issue related to the use of GTF and FASTA files during our analysis. The official examples provided in your documentation use gencode.v26lift37.annotation.gtf.gz and ucsc.hg19.f…
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I know there has been a thread about this in the past: https://github.com/trinityrnaseq/trinityrnaseq/issues/1231
but there seems to me to be an issue that isn't clearly resolved or explained.
We …
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Now I am analyzing the footprints of some TFs, however, I got the error of 'Error in stop_if_wrong_length("'seqnames'", ans_len) :
'seqnames' must have the length of the object to construct (1) or…
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I am currently conducting Whole Genome Bisulfite Sequencing (WGBS) data analysis using Bismark and plan to utilize a soft-masked genome, where all repetitive and low-complexity regions are marked with…
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Hello Dr. Cheng and community,
I recently used hifiasm to assemble a allotetraploidy genome, and my command is `hifiasm -o out -t60 --primary --h1 hic_1.fq.gz --h2 hic_2.fq.gz ccs.fastq.gz`. HiFias…
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Dear developer,
We would like to perform TWAS analysis on a plant population. Our data consists of phenotypes, whole-genome gene expression levels, and genotypes for each sample.
We do not have …
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> *[Filament](https://en.wikipedia.org/wiki/Galaxy_filament)* – A large-scale structure in the universe, consisting of a network of galaxies and galaxy clusters interconnected by dark matter and gas. …
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I have assembled a single haplotype and aligned it to the hg38 reference genome. Then, I used SVision to call structural variants (SVs). When I called SVs using each haplotype separately, both haploty…
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### System information
- Ubuntu 22.04
- 1.0.5
- Cloud
### Description of the Issue
The `format` command with `--generate-metadata` crashes for a filename that doesn't contain `GCST`, even if the …
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Hello,
I have used BRAKER3 with default parameters to annotate 3 anemone genomes and my busco scores were lower than in my genome and so I ran it again using the --busco_lineages option and it solved…