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Hi @rcedgar,
I ran URMAP in my benchmark on short-read aligners and noticed that, while it is very fast, it has low CPU usage (between 10% and 90%) regardless of `-threads N` with `N=1 4, 8, or 16`…
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Hello!
Thanks again for your great tool. I wondering what your thoughts were on the idea of replacing BLAT/pblat with a tool like [minimap2](https://github.com/lh3/minimap2) for probe alignment.
…
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Hi,
I am comparing few nanopore aligners on ONT 1D and ONT 2D data, so I would like to verify if the general commands below are correct for those types of reads
**minialign -d ref_index.mai ref.fa…
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Hello,
I am getting an error something like `unrecognizable command for -p 0.9` when I use the `-mm2_options`.
My Command is as below: Please let me know if the syntax is accurate or not. I tri…
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STAR assigns 255 to good reads, which is supposed to be reserved for "unknown." From the manual:
The mapping quality MAPQ (column 5) is 255 for uniquely mapping reads, and int(-10*log10(1-1/Nmap)) fo…
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Hey! I briefly spoke with @ksahlin at RECOMB-seq about trying out [Block Aligner](https://github.com/Daniel-Liu-c0deb0t/block-aligner). Block Aligner supports both global and extension (X-drop) affine…
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Hello,
My lab is in the process of testing out Salmon and potentially switching to it from traditional aligners. With a traditional aligner, we use picard's MarkDuplicates to remove PCR duplicates.…
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### Description of feature
I'm following up on a slack post that I put out 2 months ago at https://nfcore.slack.com/archives/CHN5BV5DW/p1712178056321859
I had a question about the fastq format nee…
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Before this change https://github.com/samtools/htslib/pull/1854 U was changed to N when read by samtools
Now it will be changed to T
However, I think it would be "better" if we could preserve U …
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Hi,
I have been trying to use cgpwgs to call the variants on my own BAM files. I saw it said the BAM files are expected to have been mapped using cgpmap. We did not use the cgpmap to get the BAM file…