User: delhomme@embl.de

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Posts by delhomme@embl.de

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Answer: A: easyRNASeq for miRNA read counts
... Hej Vicky! The very short answer is that it depends on the content of your annotation. I can?t really tell you more without knowing more about the kind of data you want to provide as input to easyRNASeq, both for the read alignments and as annotation. In my view of things using ?features? would be ...
written 4.0 years ago by delhomme@embl.de1.2k
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Answer: A: retrieving annotation
... Hej Kathi! In a different thread (GTF file error when using easyRNAseq), Martin mentioned that you can access ensemble gff files through AnnotationHub. I just copy part of this answer below and as you can see, the gene_biotype is part of the annotation: > library(AnnotationHub) > hub = Anno ...
written 4.0 years ago by delhomme@embl.de1.2k
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Comment: C: GTF file error when using easyRNAseq�
... Hej Michael, Good question really. I have a number of reason for this: 1) I?ve been using the genomeIntervals readGff3 function for that - for years now - and I?ve always been satisfied by its performance, especially when parsing the gff/gtf ninth column. The parseGffAttribute and getGffAttribute ...
written 4.0 years ago by delhomme@embl.de1.2k
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Comment: C: GTF file error when using easyRNAseq�
... Hej Natalia! There were a number of lines in that particular gtf that violated the assumptions I had about EnsEMBL gtf. Not all the fields in the attributes' column were always set and one of the gene name had a space character in it. I?ve made the parsing of gtf file annotation more flexible/lenie ...
written 4.0 years ago by delhomme@embl.de1.2k
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Answer: A: GTF file error when using easyRNAseq�
... Hej Natalia! This is not the first time that I?ve seen this error on the list, but I?ve not been able to reproduce it so far with my own data. Would you mind sharing some data offline, just an excerpt of your files would do. If that?s OK, I can create and give access to a folder on my box account. ...
written 4.0 years ago by delhomme@embl.de1.2k
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Comment: C: EasyRNAseq - error in building count table - Error in unlist
... Hej Felix! I suppose that you could use the gene_id for that. From what I've seen the biomaRt "ensembl_gene_id" and the "Parent" in the gff file below are similar. You could therefore from your query extract the "protein_coding" only and use these to subset the synthetic gene model gff file to cont ...
written 4.2 years ago by delhomme@embl.de1.2k
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Comment: C: EasyRNAseq - error in building count table - Error in unlist
... Hej Felix! I figured out what the error is: Here are the end of the exons located at the extremity of the 10 chromosomes: Browse[1]> sapply(lapply(ranges(geneModel(obj))[gm.sel],range),end) 1 10 2 3 4 5 6 7 8 9 301409969 14 ...
written 4.2 years ago by delhomme@embl.de1.2k
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Answer: A: eayRNASeq with Ensemble GRCh37 help
... Hej Aki Hoji! You can indeed ignore the warnings. The error is this: > The number of conditions: 0 did not correspond to the number of samples: 1 For using the DESeq output, you need to precise the conditions, see the ?easyRNASeq help page and the easyRNASeq and DESeq vignettes (e.g. vignette( ...
written 4.2 years ago by delhomme@embl.de1.2k
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Answer: A: EasyRNAseq - error in building count table - Error in unlist
... Hej Felix! This is strange. Would you be able to share the data offline with me so that I can try to reproduce the issue? If it's possible I would create a drop box folder. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational ...
written 4.2 years ago by delhomme@embl.de1.2k
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Answer: A: some problems of easyRNASeq� : about the gtf files
... Hej Fuyan! On 19 Mar 2013, at 05:27, Hu Fuyan [guest] wrote: > > I want to use easyRNASeq to get exon counts. But I found a strange thing: > > I have two human annotation files from different sources: one(Homo_sapiens.GRCh37.70.gtf.gz > ) is from ensemble ftp (ftp://ftp.ensembl.org ...
written 4.7 years ago by delhomme@embl.de1.2k

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