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Very strange behavior. I have four ATAC-seq samples across two experimental conditions (two each). For three of the samples, Genrich identifies ~10-30k peaks, but for the other one, it identifies 0. H…
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Hi,
How does POCP compare to Average Amino acid Identity (AAI)?
Both calculation wise and interpretative/biologically speaking.
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Hello, I apologize for the novice question but I am trying to run TAMA Collapse and then TAMA Merge on isoseq data that has been mapped to a genome, once using minimap2 and once using uLTRA with a pre…
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Hello,
I have been trying to streamline my manual curation process of TE libraries using your GUI which I think is a very nice idea.
However, when blasting the TE model against the genome, I …
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Hello,
I am using Isoquant to quantify my bam files, 6 samples (3 treatment Vs 3 control). the process seems to be frozen after some time. in the aux folder, I got OUT.save_chr (_bamstat, _collecte…
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I was wondering if there was any upper limit (either computationally or experimentally) in terms of the size of the genome(s) to run olivar on. I'm trying to design a primer set for multiple organisms…
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Hi, thanks to the development of this tool, I used short reads and HiFi reads to evaluate the genome at the same time, and although I got the final result, there seems to be some errors in the log fi…
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Hello!
Great tool, thank you!
I have completed some Nano3P'Seq, and now trying this tool to pick out some information.
I have had to convert a GFF3 file to GTF (I used gffread), and the al…
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Hello! I was running 3.0 almost successfully yesterday but it crashed during gnomon training so I updated to 3.1. Today it appears to not make it through the alignment stages with the following error:…
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Thank you for your work.
When I run vadr 1.6.3 on this virus: https://www.ncbi.nlm.nih.gov/nuccore/KY933089 (fasta file)
I obtain nothing in the 'pass' tsv file.
In the 'fail' tsv file, I get t…