User: michael.ante
michael.ante • 3.6k
- Reputation:
- 3,620
- Status:
- Trusted
- Location:
- Austria/Vienna
- Last seen:
- 2 months ago
- Joined:
- 6 years, 2 months ago
- Email:
- m***********@gmx.net
Posts by michael.ante
<prev
• 408 results •
page 1 of 41 •
next >
0
votes
1
answer
351
views
1
answers
Comment:
C: How to identify 3'UTR region?
... Hi,
it's more a vague idea: You can try to find the PAS-signal and define the region between it and the CDS as 3' UTR. The signal is usually an A-rich hexamer. You may model the genome with a similar species' 3' UTR-length distribution to limit the search space.
Cheers,
Michael ...
written 11 months ago by
michael.ante • 3.6k
0
votes
2
answers
357
views
2
answers
... Is the chromosome/config name identical in both files? Does it contain spaces like `HanXRQCP 123456bp further information`?
Are the names from the alignment altered? ...
written 11 months ago by
michael.ante • 3.6k
0
votes
1
answer
652
views
1
answers
... Hi ,
You are using the default values for quality filtering. Leading to different levels of stringency:
> __too_low_aQual 2391179
vs
> Unassigned_MappingQuality 0
The default mapping quality's minimum is 10 for htseq-count and 0 for featureCounts.
Using the same quality filter value ...
written 12 months ago by
michael.ante • 3.6k
0
votes
0
answers
266
views
0
answers
... To my understanding, having the fitting gene expression profile is the necessary condition, that a pathway might be activated in your sample. But it's not the sufficient condition. Some enzymes might be present, but in an inactive state.
To make some robust statements, you can correlate the gene ex ...
written 12 months ago by
michael.ante • 3.6k
0
votes
0
answers
266
views
0
answers
... Hi CY,
I'd guess that would be true if there is a direct relationship between gene expression and enzyme-activity (which is more or less the same for all genes).
You have also the ambiguity between gene-centered pathway annotation and expression of gene isoforms which might or might not different ...
written 12 months ago by
michael.ante • 3.6k
0
votes
1
answer
367
views
1
answers
... Apparently, there is an R-package for reading and accessing fasta files [seqinr][1].
Once having the fasta as object, you it should be easy to apply your Perl routines.
[1]: https://www.rdocumentation.org/packages/seqinr/versions/3.6-1 ...
written 13 months ago by
michael.ante • 3.6k
0
votes
1
answer
367
views
1
answers
... I guess that should be solvable by writing a script in biopython utilising the seqIO library.
Alternatively, you can try it with command line tools like awk, cut, [fasgrep][1], and join to loop over you CSV file.
[1]: https://github.com/tlawrence3/FAST/blob/master/README.md ...
written 13 months ago by
michael.ante • 3.6k
0
votes
1
answer
449
views
1
answers
... Hi Geetha,
Did you receive an error? Can you provide the first couple of lines from your input and output gtf? ...
written 13 months ago by
michael.ante • 3.6k
0
votes
1
answer
414
views
1
answers
... Usually, STAR needs a lot of RAM to align and even more to build the index. Thus, having the STAR index files properly generated, you should be able to run the alignment.
Are there any clues in the log files from STAR, what went wrong?
Have you tried it with R1 reads only?
...
written 13 months ago by
michael.ante • 3.6k
0
votes
0
answers
365
views
0
answers
Comment:
C: FASTQ exctract ID's
... Not the nicest solution, bit you can use grep to get the fastq entries:
grep -f name.lst -A 3 --no-group-separator in.fq > out.fq
The `-f` determines the name.lst entries as things to be searched for, `-A 3` leads to reporting the 3 lines **a**fter each hit. The `--no-group-separator`is not ...
written 13 months ago by
michael.ante • 3.6k
Latest awards to michael.ante
Commentator
14 months ago,
created a comment with at least 3 up-votes.
For C: Merge 2 files based on rs number but keep all info only from the first file
Commentator
15 months ago,
created a comment with at least 3 up-votes.
For C: Merge 2 files based on rs number but keep all info only from the first file
Commentator
22 months ago,
created a comment with at least 3 up-votes.
For C: Merge 2 files based on rs number but keep all info only from the first file
Commentator
2.0 years ago,
created a comment with at least 3 up-votes.
For C: Merge 2 files based on rs number but keep all info only from the first file
Commentator
2.1 years ago,
created a comment with at least 3 up-votes.
For C: Merge 2 files based on rs number but keep all info only from the first file
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: questions on rna-seq data analysis
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: questions on rna-seq data analysis
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: questions on rna-seq data analysis
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: questions on rna-seq data analysis
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: questions on rna-seq data analysis
Voter
2.9 years ago,
voted more than 100 times.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1139 users visited in the last hour