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Recent Replies
Comment: March 13-16: Virtual Nextflow and nf-core training event in 5 languages
by
Maxime Garcia
▴
210
All the videos are now online and organized in 5 different playlists on the nf-core youtube channel: https://www.youtube.com/@nf-core/playl…
Answer: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
by
Mike Smith
★
2.0k
We can take a look at the content of those three attributes to try and figure this out. Here's some code to extract each set of Agilent ID…
Comment: FastQ file not recognized by hisat2 allignment
by
Maxime Garcia
▴
210
I'd agree with you, but just to clarify. The fact that you actually used `path("fastq1")` instead of `path(fastq1)`, named the input file `…
Answer: Where do find virulence gene information in a gff/gtf file?
by
oschwengers
▴
80
You could try Bakta to annotate your bacterial genome. Internally, it uses AMRFinderPlus and VFDB and potential hits are marked in GFF3 col…
Answer: GIAB Truth Set
by
Jeremy Leipzig
21k
The truthset is an amalgam or consensus of at least 3 different sequencing technologies (Complete Genomics, 10X, Illumina). I'm not sure co…
Comment: split fasta file to train deep learning model
by
Mensur Dlakic
★
23k
This isn't what you are asking, but I will give your my opinion just in case.
If you have a single genome, doing a random 80:20 split as y…
Comment: split fasta file to train deep learning model
by
GenoMax
126k
`reformat.sh` from BBTools as well.
Sampling parameters:
reads=-1 Set to a positive number to only process thi…
Comment: Calculate RPKM
by
Chris
▴
70
I got gene_length and counts matrix with the same number of row with your suggestion.
y <-DGEList(counts=your_data_frame,genes=data.f…
Comment: Handling single-sample VCF after haplotypecaller
by
Y.H.P
•
0
Does it mean that before going through combining and final genotyping, all procedures regarding handling VCF files (ex: hard-filtering, BQS…
Answer: FastQ file not recognized by hisat2 allignment
by
Mensur Dlakic
★
23k
> No such variable: fastq1
Error messages don't come any clearer than this. Your script is expecting a variable named fastq1 to be used …
Comment: Bowtie2 parameters for best alignment
by
kalavattam
▴
90
It's not necessarily a question of "better" or not. When you perform adapter/quality trimming of reads, you're sidestepping a large part of…
Comment: msigdbr returns the same genesets for mouse as in for human,
by
e.r.zakiev
▴
30
hello Igor, thanks for the great package. How do I query for mouse sets?
`msigdbr::msigdbr(species = "Mus musculus", category = "M8")`
r…
Comment: FeatureCounts >edgeR > GO
by
Pegasus
▴
80
Thank you ATpoint, I modified the main post for more clarification;
1. "When using edgeR and Deseq2 to generate a CSV file for differenti…
Comment: just one plot appears in the shiny application not all
by
bkleiboeker
▴
310
There's nowhere near enough information/code here for us to know why only one of your many plots aren't showing up. Can you provide a repro…
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