User: NathL

gravatar for NathL
NathL20
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

<prev • 16 results • page 1 of 2 • next >
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Comment: C: How to recover 5'UTR, CDS, start codon after GTF merging ?
... Thanks a lot, it's working fine with AGAT tool ! Sorry for the delay in replying. ...
written 19 days ago by NathL20
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How to recover 5'UTR, CDS, start codon after GTF merging ?
... 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 ...
gtf annotation stringtie gffcompare cuffmerge written 28 days ago by NathL20
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Comment: C: Stringtie2: how to interpret conflicts between results
... 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 NathL20
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Stringtie2: how to interpret conflicts between results
... 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, ...
de novo annotation stringtie long-reads rna-seq written 6 weeks ago by NathL20 • updated 5 weeks ago by Kevin Blighe56k
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Comment: C: Difference between UCSC annotation files
... Thanks a lot, very helpful ! ...
written 8 weeks ago by NathL20
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Difference between UCSC annotation files
... 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' ...
assembly ucsc written 9 weeks ago by NathL20 • updated 9 weeks ago by danielschmelter80
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Comment: C: Simple Workflow of Mirna Diffrential expression in galaxy or in ubuntu
... Have you tried miARma-Seq: http://miarmaseq.idoproteins.com/ ? ...
written 6 months ago by NathL20
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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 NathL20
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IGV create genome: cytoband not working
... 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 ...
rna-seq igv written 6 months ago by NathL20
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Steps for molecular docking of antibodies / antigens
... 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 ...
immunology docking written 3.3 years ago by NathL20

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Supporter 13 days ago, voted at least 25 times.
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