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Recent Replies
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
neng
•
0
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?
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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 …
Comment: STAR aligner - how is quality and correctness tested across builds/releases?
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
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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?
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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
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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?
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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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Agree - for this kind of simple stuff I wouldn't use a tuple, but just a simple path to the split files.
Comment: building snpeff database for plant
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Can you indicate which specific files you downloaded from that link?
Comment: Alternative to PASApipeline
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I don't think there are any direct alternatives to PASA with its' concept of alignment assemblies.
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Public datasets often lack proper annotations and methods descriptions, hapering reliability. You should contact the authors to ensure that…
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I think you can do this prior the enrichment. During the differential expression analysis, just add the age (or what ever quantifiers you h…
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You could use FIMO to discover binding sites from MEME motif probability tables: https://meme-suite.org/meme/doc/fimo.html
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One way is to use BEDOPS `bedmap`:
bedmap --echo --echo-map-id --range 100 --delim '\t' B.bed A.bed > answer.bed
Via: https://github.…
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