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Here is a list of aligners that are made for long reads, add yours and see if we can come up with a unified way to use them?
https://github.com/ocxtal/minialign
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Would be great to have a list of useful references and what they're good for so we can send them to clients
Some examples:
Mick Watson's manuscript about how normal aligners miss important groups …
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I realise this is a bit beyond scope for `proActiv` but it would be helpful to have an example on how to generate a valid junction file from raw reads (using STAR or Tophat2/HISAT2 for instance) for …
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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 command below is correct for those types of reads
**graphmap align -r ref.fasta -d inpu…
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This should allow us to identify hot-spots where some aligners tend to incorrectly place reads. The required information is already generated https://github.com/csiro-crop-informatics/biokanga_align_…
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Hi,
I'm wondering how this tool is different to this older tool ? I'd be interested in using one or both in alignment based metagenomics (https://github.com/MHH-RCUG/Wochenende), where mapping qua…
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Hi!
Recently, I was doing a benchmark for the performance of long spliced reads aligners(minimap2, GMAP, GraphMap2 and deSALT), but when I was running graphmap2 (v.0.6.01) on mouse pacbio SMRT read…
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Hi,
Can you please give more details about mapq scores? I only got three unique score 0,1 and 60. As most other aligners, the highest score is usually given to the uniquely mapped read. Can you ple…
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WIth typical kallisto pseudoalignment rates of ~70% for human total ribo-depleted RNA libraries, an obvious question is what the remaining 30% of reads represent, especially when aligners like hisat2 …
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When a chimeric read pair has one end which aligns well and the other aligns with MappingQuality ==0 the algorithm breaks down and fails to mark duplicates of this template. This is because the aligne…