User: manuel.belmadani
manuel.belmadani • 50
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Posts by manuel.belmadani
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... The MEME suite provides some prokaryotic databases of different sources: http://meme-suite.org/db/motifs
You can download them here: http://meme-suite.org/doc/download.html?man_type=web
You can either follow the description back to the source database, or use those since they're in MEME format, m ...
written 7 days ago by
manuel.belmadani • 50
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... Edit: The other answer is probably a more proper way to get the gene-level matrix, using `gexpr` https://www.rdocumentation.org/packages/ballgown/versions/2.4.2/topics/gexpr and should probably be marked as accepted. I'll leave mine here in case the info is useful, but I wrote my answer thinking of ...
written 5 weeks ago by
manuel.belmadani • 50
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... You should post that in an answer and mark it as accepted so the question shows up as resolved. ...
written 6 weeks ago by
manuel.belmadani • 50
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... It seems like the initial report of those flanking CTCF sites are from this [paper][1]:
"Recent studies have identified binding sites for CTCF as essential components of vertebrate insulator elements [21,22,23,24]. **CTCF-binding sites are about 50 bp and variable**, possibly because CTCF can use ...
written 8 weeks ago by
manuel.belmadani • 50
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... I got a reply from an SRA curator:
> The PATH2 is intended to be the full SRA Run accession, and is not
> restricted to a character limit.
So it appears that doing `PATH2=${SRR:0:10}` is not necessary or requested by any convention, and would probably indeed break if 11-character long identi ...
written 9 weeks ago by
manuel.belmadani • 50
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... Thanks for the reply!
I agree that what NCBI choses to do is speculative, however, wonderdump.sh *explicitly* truncates the SRR portion at 10 characters to create PATH2, when currently there's no difference between doing this and returning the full SRR. I'm assuming there's a good reason for this p ...
written 9 weeks ago by
manuel.belmadani • 50
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... I've been using [wonderdump.sh][1] from the Biostars handbook for some time. I'm now curious about the part that builds the ftp site url:
PATH1=${SRR:0:6}
PATH2=${SRR:0:10}
URL="ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${PATH1}/${PATH2}/${SRR}.sra"
I've seen SRR ...
written 9 weeks ago by
manuel.belmadani • 50
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... Keep them separated, like Nicolas said, most modern NGS software should handle paired-end reads. One they're aligned, you should have a single SAM/BAM file containing reads from both ends.
Depending on your purpose, you may need to choose different tools. For variant calling using whole-genome-sequ ...
written 3 months ago by
manuel.belmadani • 50
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Answer:
A: Annovar using VCF file
... As @Sam pointed out, you're missing the -out before myanno. The -vcfinput argument (which you had in the second command but not your first) is also necessary, and omitting it wouldn't cause the "Syntax error" message, but instead all your variants would get discarded (and written to myanno.invalid_ ...
written 2.5 years ago by
manuel.belmadani • 50
Latest awards to manuel.belmadani
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
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