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Recent Replies
Answer: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
neng
▴
30
Ok, I finally find the solution. I would like to share with you guys:
workflow {
// Step 7: split
SplitFasta(params.fasta)…
Answer: differential exon usage from Salmon outputs
by
Gordon Smyth
★
7.9k
If you want to detect differential splicing using edgeR with Salmon output, then you should do DTU instead of DEU, see:
Baldoni PL#, Chen …
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
neng
▴
30
Yeah, it's a good solution I've tried. The only problem is that the SplitFasta() process has to be finished before it starts, otherwise it …
Comment: differential exon usage from Salmon outputs
by
dsull
★
7.5k
Providing each exon as an individual transcript will throw off pseudoalignment-type algorithms which assume that each read originated from …
Comment: Create local Blast database alias with blastdb_aliastool fails
by
GenoMax
151k
Can you set the following variable and see if that helps.
BLASTDB=f:/BlastDB/nr/nr
export BLASTDB
Comment: building snpeff database for plant
by
analyst
▴
60
Is it safe to add -noCheckCds -noCheckProtein in the command or will it skip important information in the resultant database:
java -Xm…
Comment: Create local Blast database alias with blastdb_aliastool fails
by
etienne
•
0
Thank you. It is working now with:
blastdbcmd -db f:/BlastDB/nr/nr -taxids 1988 -out f:/BlastDB/extract/acti3.fa
But it displays thi…
Comment: Pathway enrichment analysis on time-series data by filtering out age comparisons
by
fullycratered
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Ah that makes sense, I hadn't done the DE analysis myself in this case. I will look at doing that, thank you!
Comment: building snpeff database for plant
by
lieven.sterck
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I had a quick look and though it is feasible to change files (and specifically feature names) such that the files correspond to each other …
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
neng
▴
30
what I expected:
[part_001, /path/to/split/part_001.fasta]
[part_002, /path/to/split/part_002.fasta]
...
actually data stream…
Comment: STAR aligner - how is quality and correctness tested across builds/releases?
by
GenoMax
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> Coming from a software engineering background
Curious as to how many people were part of your team in (I assume) commercial software dev…
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
Pierre Lindenbaum
166k
I don't understand how your splitfasta works, the output should collect the files under "split". It should be something like:
```
process …
Comment: STAR aligner - how is quality and correctness tested across builds/releases?
by
Arthur
•
0
Fair question - I single out STAR as I believe it's a widely used tool, but I am curious across the board of these 'widely used bioinformat…
Comment: RNA-Sequencing Analysis when control samples paired-end and tumour samples singl
by
h
•
0
Thanks for both your help I will do that!
Comment: STAR aligner - how is quality and correctness tested across builds/releases?
by
dsull
★
7.5k
Just curious: why do you want this documentation and why are you singling out STAR? Can you find this documentation for other bioinformatic…
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