User: manuel.belmadani

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Canada
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pragmatwit
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Posts by manuel.belmadani

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Prokaryotic protein binding motifs databases
... 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.belmadani50
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Answer: A: Generating FPKM matrix accross all samples after stringtie
... 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.belmadani50
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Comment: C: STAR alignment error- Segmentation fault (core dumped)
... 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.belmadani50
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Answer: A: Find the genomic position of CTCF binding site on DMPK gene
... 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.belmadani50
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Answer: A: wonderdump.sh and FTP site URL conventions for SRR identifiers
... 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=${SRR:0:10}` is not necessary or requested by any convention, and would probably indeed break if 11-character long identi ...
written 9 weeks ago by manuel.belmadani50
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Comment: C: wonderdump.sh and FTP site URL conventions for SRR identifiers
... Thanks for the reply! I agree that what NCBI choses to do is speculative, however, wonderdump.sh *explicitly* truncates the SRR portion at 10 characters to create PATH2, when currently there's no difference between doing this and returning the full SRR. I'm assuming there's a good reason for this p ...
written 9 weeks ago by manuel.belmadani50
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wonderdump.sh and FTP site URL conventions for SRR identifiers
... I've been using [wonderdump.sh][1] from the Biostars handbook for some time. I'm now curious about the part that builds the ftp site url: PATH1=${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 ...
ncbi ftp convention sra wonderdump written 9 weeks ago by manuel.belmadani50
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Answer: A: NGS analysis: how to handle paired-end reads
... 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.belmadani50
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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.belmadani50

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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