User: NathL
NathL • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- France
- Last seen:
- 1 week, 1 day ago
- Joined:
- 3 years, 11 months ago
- Email:
- n**********@hotmail.fr
Posts by NathL
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... Thanks a lot, it's working fine with AGAT tool ! Sorry for the delay in replying. ...
written 19 days ago by
NathL • 20
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... Hi all,
I built a new annotation file out of long reads data with `StringTie`. When I opened the resulting GTF file, I noticed that all features except **exons** and **transcripts** disappeared. So we lose all the data on **5' or 3'UTR, CDS, start** and **stop codons.**
I wonder if merging them ...
written 28 days ago by
NathL • 20
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... Thanks for your reply. That's what I am investigating now. I wondered if this was an expected behavior of Stringtie, but it seems that it's not so obvious. ...
written 5 weeks ago by
NathL • 20
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... Hi,
I am using Stringtie2 in order to obtain a better annotation of chicken genome (galGal6) using long-reads data (oxford nanopore = ONT). I visualized some gene of interest with IGV, but I found there are some conflicts that I am struggling to interpret.
First example:
In the first example, ...
written 6 weeks ago by
NathL • 20
• updated
5 weeks ago by
Kevin Blighe ♦ 56k
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... Thanks a lot, very helpful ! ...
written 8 weeks ago by
NathL • 20
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... I could not find any information on 1) how are built the annotation files that one can find in UCSC database and 2) what's the difference between the different annotation files they offer.
Do someone know if they have their own pipeline to build an annotation ? Can we find instructions of how they' ...
written 9 weeks ago by
NathL • 20
• updated
9 weeks ago by
danielschmelter • 80
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... Have you tried miARma-Seq: http://miarmaseq.idoproteins.com/ ? ...
written 6 months ago by
NathL • 20
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Comment:
C: bulk analysis by seurat
... Can you show more of your code and the first lines of your input ? ...
written 6 months ago by
NathL • 20
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... I am building a genome file to visualize chicken data. I downloaded galGal6 genome and GTF from UCSC website and followed the instructions here: https://software.broadinstitute.org/software/igv/LoadGenome. I also want to add a cytoband, and downloaded a cytoband file from ucsc table browser as descr ...
written 6 months ago by
NathL • 20
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... Hi,
I am trying to build a tool for molecular docking of antibodies and antigens. This is for a student project, and as I don't know a lot about immunology, I wanted to check with you all what do you think of the approach I am using, and advices on what could be added / improved / removed.
Input ...
written 3.3 years ago by
NathL • 20
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