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User: nlehmann

gravatar for nlehmann
nlehmann • 100
Reputation:
100
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Location:
France
Twitter:
@NathalieLehman
Last seen:
1 month, 2 weeks ago
Joined:
4 years, 3 months ago
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n**********@hotmail.fr

Posts by nlehmann

<prev • 43 results • page 1 of 5 • next >
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Comment: C: Is there a way to change gene_id in a GTF file where gene_id is actually a gene_
... Do you make such a difference with datasets from NCBI vs Ensembl ? Which database do you consider is best ? ...
written 6 weeks ago by nlehmann • 100
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Comment: C: Is there a way to change gene_id in a GTF file where gene_id is actually a gene_
... I am using both annotations as they show some differences and wanted to compare them. So I counted how many gene names that had multiple gene IDs, and we have 56 genes in this situation. Just as a matter of reproducibility, here is how I found these 56 genes: Data: # mart_export.txt example ...
written 6 weeks ago by nlehmann • 100
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Comment: C: Best way to change gene_id in a GTF file where gene_id is identical to gene_name
... It doesn't answer the question, I'll edit it to make it clearer ...
written 6 weeks ago by nlehmann • 100
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Is there a way to change gene_id in a GTF file where gene_id is actually a gene_name (and multiple genes have the same gene names) ?
... I downloaded a [GTF](https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/genes/) file from UCSC and I observed that all gene_id are identical to gene_names. Considering some genes have the same name but not the same ID and that it causes troubles with some tools, what is the best way to fix t ...
assembly rna-seq ucsc written 6 weeks ago by nlehmann • 100
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Comment: C: Detect discrepancies in GFF files
... Yes, there are 2 close by CCL4 genes, but does it really make sense ? I guess that using a better geneID instead of geneName would prevent (some of) these errors. Do you know of a tool to directly integrate geneID from Ensembl to these GTF annotations files ? ...
written 7 weeks ago by nlehmann • 100
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Comment: C: Comparisons of genes coordinates
... Yes, but it just gives genes that overlap between the 2 inputs, with no details on the way they overlap. ...
written 7 weeks ago by nlehmann • 100
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Comment: C: Detect discrepancies in GFF files
... Thanks a lot for your replies. I will try with GFF3toolkit and agat_convert_sp_gxf2gxf.pl then. Here is how to reproduce the errors: > wget https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/genes/galGal6.ncbiRefSeq.gtf.gz > gffread -E --keep-genes galGal6.ncbiRefSeq.gtf -o- ...
written 7 weeks ago by nlehmann • 100
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Comment: C: Detect discrepancies in GFF files
... We're talking about chicken genome annotation from UCSC with NCBI RefSeq annotation. To get it: `wget https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/genes/galGal6.ncbiRefSeq.gtf.gz`. A simple grep of CCL4 (case #1 about transcripts orientations) or RAP1GAP2 (case #2 about chromosomes num ...
written 7 weeks ago by nlehmann • 100
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Detect discrepancies in GFF files
... Hello, Is there a way to detect discrepancies in GFF files such as: 1- A gene has 3 transcripts, 1 is oriented on the forward strand, 2 are oriented on the reverse strand. I tried with [Gffread](http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread), but it just affects the value of the first t ...
agat gffread rna-seq ucsc written 7 weeks ago by nlehmann • 100 • updated 6 weeks ago by Biostar ♦♦ 20
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Comparisons of genes coordinates
... Hi, I would like to compare genes coordinates between 2 GTF/GFF files. I tried using [Gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) but the classification codes depends on the introns chains. I thought of something simpler, that would compare gene lengths and say if genes ar ...
gene rna-seq written 7 weeks ago by nlehmann • 100

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