User: manuel.belmadani
manuel.belmadani • 980
- Reputation:
- 980
- Status:
- Trusted
- Location:
- Canada
- Twitter:
- pragmatwit
- Scholar ID:
- Google Scholar Page
- Last seen:
- 53 minutes ago
- Joined:
- 3 years, 10 months ago
- Email:
- m***************@gmail.com
Posts by manuel.belmadani
<prev
• 117 results •
page 1 of 12 •
next >
6
votes
1
answer
57
views
1
answers
Answer:
A: VCF File type
... That group is called the "genotype", and yes, you could have `2` or higher if there's 2 or more non-reference alleles, and you can have a pipe `|` instead of `/` if the genotype is phased.
> GT genotype, encoded as alleles values separated by either of ”/” or
> “|”, e.g. The allele values are ...
written 17 hours ago by
manuel.belmadani • 980
2
votes
3
answers
235
views
3
answers
... Your reads would be in FASTQ format, not FASTA, though you will possibly have a transcriptome/genome reference in FASTA format.
A typical workflow I would say is something like:
- Start with by getting some FASTQ files, have them in separate directories per sample (this is something that's done e ...
written 11 days ago by
manuel.belmadani • 980
0
votes
0
answers
102
views
0
answers
... Maybe this isn't exactly what you're looking for but, but GSE20346 has been re-processed and analyzed on our Gemma database:
- Experiment page: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=3023
- Controls are shown here: https://gemma.msl.ubc.ca/experimentalDesig ...
written 12 days ago by
manuel.belmadani • 980
0
votes
1
answer
184
views
1
answers
... You can actually replicate what InterVar tells you with the VarSome UI.
Example:
PVS1=0
PS=[0, 0, 0, 0, 0]
PM=[0, 1, 0, 0, 0, 0, 0]
PP=[0, 0, 1, 0, 1, 0]
BA1=0
BS=[0, 0, 0, 0, 0]
BP=[1, 0, 0, 0, 0, 0, 0, 0]
![enter image description here][1]
Why do they get different information? I'm not too fam ...
written 13 days ago by
manuel.belmadani • 980
1
vote
1
answer
161
views
1
answers
Answer:
C: Novel peptide identification
... Do you mean that you have 30,000 distinct peptides that you want to search or you have one (or more) peptides of length 30,000 (i.e. 30,000 characters long)?
I think you probably mean 30,000 peptides, and I assume your peptides are probably pretty short, i.e. as short as 2 amino acids to dozens, ...
written 19 days ago by
manuel.belmadani • 980
2
votes
1
answer
153
views
1
answers
... Did you try running the script they provided?
https://github.com/akram-mohammed/septic_shock_degs/blob/master/sepsisGenomics_DGE.R ...
written 4 weeks ago by
manuel.belmadani • 980
0
votes
0
answers
99
views
0
answers
... Can you plot and show the distribution of p-values for your genes? Is it flat? ...
written 5 weeks ago by
manuel.belmadani • 980
0
votes
2
answers
135
views
2
answers
Comment:
C: All result in one file
... Which one? Does it give you an error message or it doesn't merge them properly?
The main problem I see is that you're getting `res` from biomart. So calling `res[[k]]` doesn't seem to make sense since biomart doesn't know that you have `k` files, that's why I assumed you were using `i` in `res[[i]] ...
written 5 weeks ago by
manuel.belmadani • 980
1
vote
2
answers
135
views
2
answers
Answer:
A: All result in one file
... The easiest way to fix that would be to change your filename as you're writing is, for example:
write.csv(res[[i]], file = paste0("recovery_gene_trans_",k,".txt"))
So for each `k` file, your file name with be suffixed with `k.txt`.
But what is `i` here? it shows up in your `write.csv` but do ...
written 5 weeks ago by
manuel.belmadani • 980
• updated
5 weeks ago by
zx8754 ♦ 7.8k
2
votes
2
answers
188
views
2
answers
... It does provide transcript level TPM since 2015:
> 10/19/2015 - v1.1.0 release This StringTie release includes the
> following updates: major memory usage improvements due to: changes of
> internal data structures, collapsing reads aligned in the same place
> and filtering of spurious s ...
written 6 weeks ago by
manuel.belmadani • 980
Latest awards to manuel.belmadani
Good Answer
17 hours ago,
created an answer that was upvoted at least 5 times.
For A: Reproducing this plot in R
Scholar
17 hours ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Teacher
17 hours ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Centurion
9 weeks ago,
created 100 posts.
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
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
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Good Answer
5 months ago,
created an answer that was upvoted at least 5 times.
For A: Reproducing this plot in R
Scholar
5 months ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Supporter
5 months ago,
voted at least 25 times.
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Scholar
6 months ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Scholar
6 months ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: NGS analysis: how to handle paired-end reads
Scholar
12 months ago,
created an answer that has been accepted.
For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
Scholar
13 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: 1562 users visited in the last hour