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Recent Replies
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!
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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
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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
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Pierre Lindenbaum
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I don't understand how your splitfasta works, the output should collect the files under "split". It should be something like:
```
process …
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by
Arthur
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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
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Thanks for both your help I will do that!
Comment: STAR aligner - how is quality and correctness tested across builds/releases?
by
dsull
★
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Just curious: why do you want this documentation and why are you singling out STAR? Can you find this documentation for other bioinformatic…
Comment: building snpeff database for plant
by
analyst
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60
1. sequences.fa (genomic.fna.gz file)
2. genes.gff.gz (genomic.gff.gz file)
3. genes.gtf.gz (genomic.gtf.gz file)
4. protein.fa.gz (protei…
Comment: SPAdes assembler k-mer > default 127 possible?
by
owen.donohoe
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Thanks, these comments are very useful. We ran into installation and memory problems with this process (spades v3.15.2), but we eventually …
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
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colindaven
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Agree - for this kind of simple stuff I wouldn't use a tuple, but just a simple path to the split files.
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