User: manuel.belmadani

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Posts by manuel.belmadani

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Interpreting stats from gnomAD/ ExAC reference population
... The easiest way I see is to download the raw data in VCF (variant calling files) format ([Sites VCF][1]) and use some kind of tool that summarizes VCF files. ([Example][2], haven't tried it.) To do anything serious, most likely you would have to use some programming/scripting language. R is great ...
written 8 weeks ago by manuel.belmadani60
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Answer: A: annotate and analyse mutation from cosmic
... You can download the COSMIC mutations from the [COSMIC download page.][1] Get the [VCF][2] format files from "VCF Files (coding and non-coding mutations)". VCF files are "variant calling" files, meaning they contain variant (mutation) positions and annotations. Your TF ChIP-Seq data may be formatt ...
written 8 weeks ago by manuel.belmadani60
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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 10 weeks ago by manuel.belmadani60
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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 3 months ago by manuel.belmadani60
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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 3 months ago by manuel.belmadani60
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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 4 months ago by manuel.belmadani60
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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=${SRR:0:10}` is not necessary or requested by any convention, and would probably indeed break if 11-character long identi ...
written 4 months ago by manuel.belmadani60
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Comment: C: wonderdump.sh and FTP site URL conventions for SRR identifiers
... Thanks for the reply! I agree that what NCBI choses to do is speculative, however, wonderdump.sh *explicitly* truncates the SRR portion at 10 characters to create PATH2, when currently there's no difference between doing this and returning the full SRR. I'm assuming there's a good reason for this p ...
written 4 months ago by manuel.belmadani60
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wonderdump.sh and FTP site URL conventions for SRR identifiers
... I've been using [wonderdump.sh][1] from the Biostars handbook for some time. I'm now curious about the part that builds the ftp site url: PATH1=${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 4 months ago by manuel.belmadani60
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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 5 months ago by manuel.belmadani60

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Scholar 3 months ago, created an answer that has been accepted. For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Scholar 4 months ago, created an answer that has been accepted. For A: wonderdump.sh and FTP site URL conventions for SRR identifiers

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