User: Florian Bernard

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Posts by Florian Bernard

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Use Salmon to annotate a Sam file
... Honestly I've looked through Salmon's documentation before, and once more, but I can't find any parameters to do what I want to do. Maybe it's just a matter of wording but it would be nice if you could direct me toward what you meant. The closest thing I found is --writeMappings but it doesn't work ...
written 13 months ago by Florian Bernard70
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Use Salmon to annotate a Sam file
... Hi, I was wondering if there was any way to use Salmon to annotate the Sam file, like adding a Tag that says to which transcript the read is mapping to. I think it was a feature available with featureCounts but I can't seem to find anything like that in the documentation of Salmon. And I want to ke ...
alignment quantification salmon rna-seq written 13 months ago by Florian Bernard70 • updated 13 months ago by ATpoint36k
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retrieve relative position of CDS start for every isoforme
... For every isoformes in C. elegans, I would like to get a table that look like that : transcript CDS start ZK993.1b.1 ZK993.1b 40 ZK993.1b.2 ZK993.1b 20 I tried to parse a gtf file, extract the start positions for each transcript and the position for ...
rna isoforme written 16 months ago by Florian Bernard70
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Comment: C: Best practices for counting genes with nanopore RNAseq data
... Salmon now being recommended by ONT and used in several papers, it seems it was a good call ! Thanks for your help. ...
written 17 months ago by Florian Bernard70
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Comment: C: How to identify long reads coming from ligated cDNAs before sequencing ?
... Yes, based on this definition of chimeric reads here [https://www.biostars.org/p/153461/#153467][1] > Correct, a chimeric (or "non-linear") alignment occurs when > non-overlapping portions of it map to (A) different portions of the > same chromosome in a manner not normally biologically su ...
written 17 months ago by Florian Bernard70
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Comment: C: How to identify long reads coming from ligated cDNAs before sequencing ?
... Yes you are right, I'm actually trying to see if it worked or not.. (hence: to see if there is a point to do that supplementary step or not). But being novice at bioinformatics I'm not sure if what I'm observing comes from an erroneous way of analyzing my dataset or if there is indeed no real differ ...
written 17 months ago by Florian Bernard70
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How to identify long reads coming from ligated cDNAs before sequencing ?
... We have generated sequencing data with the direct-cDNA sequencing kit from ONT. During the library prep, prior to adding the adapters on each cDNA, we performed a ligation step to concatenate cDNAs together. The aim was to see if we could increase the total number of cDNAs sequenced whithout actua ...
minimap2 cdna alignment nanopore ont written 17 months ago by Florian Bernard70
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Comment: C: Best practices for counting genes with nanopore RNAseq data
... Ok that's interesting and definitely worth a try ! I'll came back to report how it went, thanks ! ...
written 18 months ago by Florian Bernard70
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Comment: C: Best practices for counting genes with nanopore RNAseq data
... I've been using the -o option already (I need it for a downstream analysis) but even if i manage to distinguish reads that are being counted from reads that are not, how will I be able to say why ? ...
written 18 months ago by Florian Bernard70
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Comment: C: Best practices for counting genes with nanopore RNAseq data
... It might be a naive question but I read that in Salmon's documentation : > Salmon expects that the reads have been aligned directly to the > transcriptome (like RSEM, eXpress, etc.) rather than to the genome (as > does, e.g. Cufflinks). I don't get the point of first maping against the tr ...
written 18 months ago by Florian Bernard70

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