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Hello,
I'm also keen to integrate into the genome graph the structural variability detected by Sv callers (from short reads and/or long-reads). I was wondering if minigraph handles that?
Those are …
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Here are suggested new indexing parameters for all read lengths.
This supersedes #397.
I ran the optimization script for both v0.12.0 (commit 6fd4c5d) and multi-context seeds (commit c4a7f61).
…
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Hello,
Thank you for setting up this repo! I was wondering if this data has been published yet and if so what paper we can cite to use this data?
Cheers,
Richard
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I have been using STAR with Illumina 101bp paired end reads. The first set of
libraries I sequenced work great going through the pipeline, but I have had a
very strange problem with the most rec…
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Things to check:
* [ ] What does stellar do with long repeat regions (i.e. a whole 1Mb sequence only containing "A")
* Does it have more than one Swift Verification?
* [ ] Have benchmarks and sim…
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We're developing a project that makes use of your library (and the C# official wrapper). Our project can get big benefits with some libplctag library optimizations and additions. If this library have …
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If the extend_read value is smaller than certain reads, those should not be affected. Right now, those are shrunk.
An appropriate test is commented out at the end of the test.metagene_extend_reads …
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Based on the methods in the Draft Human Pan-Genome paper (https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1) it looks like BAM files surjected from giraffe graph alignments (which it appears…
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Hi all,
I am trying out Magic-BLAST for mapping short-reads, and may want to test it in various pipelines.
I noticed, however, that the MAPQ field in the SAM output is either 0 or 255.
At fir…
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We’ve been getting some odd results in a single cell study and tracked these down to a set of genes which had odd clusters of mapped regions over only part of one exon of the gene.
When we looked at …