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Hi,
I am attempting to perform a genome-guided assembly using Trinity. I have a BAM file aligned to the genome, and the command I used is:
singularity exec --bind /work /home/software/containers/tri…
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Hi,
Is VACmap set up to do genome vs genome alignments? I could run in -mode L, however an assembled genome would have much fewer errors.
thanks.
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I've been trying to use this program to run an MK test using VCF files from the 1000 genomes project. However, I'm getting some really strange results with this method, and I'm worried I may be doing …
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Hi,
Thanks for developing phastSim - a lovely tool.
I just have a quick question regarding how phastSim adjusts genomic positions when insertions and deletions are added to the genomes: when sub…
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It would be great to have an (optional) module in the pipeline that generates coverage data for species of interest (e.g., all human infecting pathogens with greater than X number of hits).
Ideall…
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Hello,
I'm using seq_io to do some sliding window analysis of a 4Mb genome, but the size of the sequence remains limited. How should I configure my Rust program for the seqeunce size to be about 4M…
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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, very nice tool - well done! Any plans for supporting cram files? It looked like you are using `samtools` for handling alignments, but one would then presumably need to pass along a reference genom…
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### Description of feature
Hi Jason,
This workflow looks great and I hope to try it out soon.
If you haven't already considered it, you might want to take a look at incorporating this tool as an a…
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Hi, this project looks good! Thanks!
I would like to use Tark as a source of transcripts for [Biocommons HGVS Python library](https://github.com/biocommons/hgvs)
RefSeq transcripts can differ fr…