User: Florian Bernard

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Posts by Florian Bernard

<prev • 24 results • page 1 of 3 • next >
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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 9 weeks ago by Florian Bernard50
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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 3 months ago by Florian Bernard50
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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 4 months ago by Florian Bernard50
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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 4 months ago by Florian Bernard50
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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 4 months ago by Florian Bernard50
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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 4 months ago by Florian Bernard50
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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 4 months ago by Florian Bernard50
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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 4 months ago by Florian Bernard50
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Comment: C: Best practices for counting genes with nanopore RNAseq data
... Then if it's all the same, since I'm more interested by reads that have been assigned to a gene, can we say that `HTseq + intersection-nonempty` produce the more useful result ? At the same time I'm worried that I might be working with reads wrongly assigned.. Having very little experience in bioin ...
written 4 months ago by Florian Bernard50
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Best practices for counting genes with nanopore RNAseq data
... Hi, I searched the previous posts and the nanopore community forum but couldn't find a definitive answer so here I am looking for your advice. I know working with long-reads RNA-seq data is still complicated because it's hard to find a general consensus on how to analyse them but I'd be interested ...
alignment rna-seq nanopore written 4 months ago by Florian Bernard50 • updated 4 months ago by h.mon26k

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