User: jhb80

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jhb8040
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Posts by jhb80

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Comment: C: noncoding RNA list of mouse mm9
... You can use the standard (=comprehensive) gtf file. The GENCODE gtf contains Ensemble-based transcript- and gene-biotype information. You can then pull out the transcript- (or gene-) identifiers for all different types of non-coding RNA you're interested. Check out http://www.gencodegenes.org/mouse_ ...
written 2.6 years ago by jhb8040
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Answer: A: noncoding RNA list of mouse mm9
... Long, small or both types of ncRNA? I'd suggest GENCODE (http://www.gencodegenes.org/mouse_releases). Version M1 is based on mm9, but the more up-to-date versions (currently M9) are based on mm10. NONCODE (http://www.noncode.org/) is another good source / reference collection. ...
written 2.6 years ago by jhb8040
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Comment: C: Current state-of-the-art for RNA-Seq gene / transcript expression quantification
... Hi Devon & Co. - I just stumbled over the manual for DESeq2 v1.11.23, which mentions the option to use transcript-level abundance information from e.g. kallisto, sailfish or salmon. Curious if anyone has had a chance to try that out and can comment on the performance...? This would be a really ...
written 2.6 years ago by jhb8040

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