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I was wondering if anyone has any recommendations for using tombo resquiggle to allign fast5 files to a subset of a reference genome rather than mapping to a whole reference. In particular, we have b…
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Dear developers,
Many thanks to your group for providing such excellent tool for RNA-seq analysis. Here i have a question that have confused me quite a while.
I created two versions of genome i…
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Dear KVD-lab,
I appreciate your large effort to maintain and update PuMA.
I met some trouble with a Docker version of PuMA v1.2.1 . Processing PaVE's HPV41REF.1 occurs the following error:
``…
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Hi,
I am dealing with a large genome and therefore running quickmerge took a very long time, is there a way to run the quickmerge wrapper in multi-thread to accelerate the process? I check the wrap…
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- what is the smallest test data we can use?
- download large testdata where needed
- include small intermediate files in `tests/test-data` wherever possible
- see https://github.com/dib-lab…
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Hi,
Please describe:
1. What you were trying to do
I aligned a whole genome sequencing data set to a human genome augmented with SNPs and indels. Then I aligned the same dataset to the same gra…
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We're trying to optimize alignments of oligos (~ 21 bp). We tried setting --sjdbOverhang and --genomeSAindexNbases using STAR 2.7.10a. We are trying to build the index using the NCBI human reference…
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#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify.
(ru…
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## Short description of the problem
I created a genomes storage consisting of ~2k genomes, and when I tried to run `anvi-pan-genome`, it exceeds my disk quota on the cluster and the job fails. It c…
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Hi there,
I created a dotplot with pafR to compare large genomes,
altough I can't really read the dotplot since the lines of the figure (the raster) makes it hard
to see where the genomes are sim…