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Recent Replies
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
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dthorbur
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You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
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emilydolivo97
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I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
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As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
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rohitsatyam102
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As per the image below obtained by Running RNASeQC the intronic reds aren't that much (See the knockdown samples enclosed in the Red box) (…
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Am I understanding this correctly, that what you are looking for is any sequence where *any part* of the coord range overlaps with *any oth…
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edoardofilippi1998
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Did you check the data in the assay of the cell_data_set object?
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use the output of `samtools mpileup`
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It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
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Dora
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Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
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Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
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Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
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analyst
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It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
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Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
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Pierre Lindenbaum
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again, remove the spaces " "SOR > 10." -> " "SOR>10"
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