User: manuel.belmadani
manuel.belmadani • 70
- Reputation:
- 70
- Status:
- Trusted
- Location:
- Canada
- Twitter:
- pragmatwit
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 3 years, 4 months ago
- Email:
- m***************@gmail.com
Posts by manuel.belmadani
<prev
• 11 results •
page 1 of 2 •
next >
0
votes
1
answer
485
views
1
answers
... 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 4 months ago by
manuel.belmadani • 70
0
votes
1
answer
291
views
1
answers
... 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 4 months ago by
manuel.belmadani • 70
0
votes
1
answer
179
views
1
answers
... 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 5 months ago by
manuel.belmadani • 70
2
votes
2
answers
975
views
2
answers
... 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 6 months ago by
manuel.belmadani • 70
0
votes
0
answers
690
views
0
answers
... You should post that in an answer and mark it as accepted so the question shows up as resolved. ...
written 6 months ago by
manuel.belmadani • 70
1
vote
3
answers
279
views
3
answers
... 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 7 months ago by
manuel.belmadani • 70
1
vote
1
answer
299
views
1
answers
... 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=${SRR:0:10}` is not necessary or requested by any convention, and would probably indeed break if 11-character long identi ...
written 7 months ago by
manuel.belmadani • 70
0
votes
1
answer
299
views
1
answers
... Thanks for the reply!
I agree that what NCBI choses to do is speculative, however, wonderdump.sh *explicitly* truncates the SRR portion at 10 characters to create PATH2, when currently there's no difference between doing this and returning the full SRR. I'm assuming there's a good reason for this p ...
written 7 months ago by
manuel.belmadani • 70
2
votes
1
answer
299
views
1
answer
... I've been using [wonderdump.sh][1] from the Biostars handbook for some time. I'm now curious about the part that builds the ftp site url:
PATH1=${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 7 months ago by
manuel.belmadani • 70
3
votes
3
answers
1.2k
views
3
answers
... 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 8 months ago by
manuel.belmadani • 70
Latest awards to manuel.belmadani
Scholar
6 months ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Scholar
7 months ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1315 users visited in the last hour