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Forum: Snakemake vs. Nextflow: strengths and weaknesses

forum snakemake nextflow written 3 days ago by ropolocan • 230 • updated 3 days ago by Sinji • 2.4k

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Tool: NextflowWorkbench: An integrated development environment for workflows

lwt tools workflow nextflow workbench written 21 months ago by fac2003 • 160 • updated 21 months ago by Istvan Albert ♦♦ 71k

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Epic Question to lh3 ♦ 29k
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Recent Replies

C: Partial protein Sequence by jrj.healey • 1.6k
Just put them through BlastP?
A: GTF file: CDS feature is exon 1, but has frame = 1 or 2 by Devon Ryan ♦ 68k
For genes on the `-` strand, you don't want exon 1, but the last exon. You'll note it has frame 0.
C: List of all enhancers found in mouse genome by genomax ♦ 29k
See this: https://www.biostars.org/p/157223/ You should also try BioMart and the Ensembl regula...
C: Plot of up and down regulated metabolic pathways in this way by khhgng • 30
Thanks. I am new to such analysis and R so its difficult to follow the methods section exactly. T...
C: What is each sequence valid identifier by genomax ♦ 29k
Simply put a valid fastq record will always need to have 4 lines. The first line should start wit...
C: How to perform edgeR based on serial paired samples? by vchris_ngs • 3.4k
Ah nice, this is nice. Have not had paired data for a while probably that is the reason I was con...
C: What is each sequence valid identifier by Devon Ryan ♦ 68k
Again, such files are so obscure and old (I've never even seen one and I've been doing this for a...
C: How to perform DESeq2 based on paired sample test? by Devon Ryan ♦ 68k
You're using DESeq2, so `counts(dds, normalized=T)` will give you more useful values.
C: How to perform edgeR based on serial paired samples? by Devon Ryan ♦ 68k
The pairing already took place in the model fit, so unless someone wants to look at per-subject c...
C: How to perform DESeq2 based on paired sample test? by Xiaokang ZH • 20
I've deleted those two samples completely, including the levels 1 and 7 in fishGroup: > l...
A: Visualising BedGraph files on UCSC [custom tracks] by arup • 10
The bedGraph file you have don't use the correct formatting. A standard bedGraph file will be lik...
A: STAR Indexing problems with unassambled vertebrate genomes by colindaven • 180
I'd make a STAR reference without the GTF/gff3 annotation included. These formats are notoriousl...

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