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**Use case**
I run macs2 with below command per q-value cut-off 0.05, 0.1 and 0.5
`macs2 callpeak -f BAMPE -g hs -n sample_ID -t sample_remove_duplicate_mito.bam --outdir ./peak --min-length 100 --q…
khsjh updated
9 months ago
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Is there a way to use FusionInspector so that all fusion gene candidates are written out without filtering? max-sensitivity and extreme-sensitivity are still cutting some fusions out
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Hi, I have a question about how reads are assigned as conflicting, unassignable etc.
I've been trying to use SNPsplit on noisy PacBio long reads to help with haplotype-resolved assembly (which I kn…
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Hi, I get an error while trying to run Guava for differential analysis, saying samtools not found, or something like that, even though I'm pretty sure its installed.
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I tried sniffles2 on some Nanopore data (see picture) with a homozygous RhD deletion. Sniffles1 did call this deletion (min supporting reads 3) and I tried using the exact same parameters on Sniffles2…
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Would it be possible to view th…
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Hello,
I have the issue that two obvious variations are not called. This is WGS nanopore sequencing of a transgenic mouse. The region in question is alien sequence (human for the most part) that wa…
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We should look at developing a tool or option into ngsmapper, unless one is already in dev that automates finding the PCR bias in reads. Currently the options are (i) hard crop the reads which could s…
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Hi Rob. I'm using the `--writeMappings` option in Salmon 0.7.2, but reporting this issue here since I think the code base is (will be) the same. I have a few genes that we've noticed (based on biologi…