User: elsoja

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elsoja70
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Posts by elsoja

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Comment: C: RNA-Seq quantification of a heterozygous individual with a short deletion
... Thank you, Lior! That's what I'm doing right now. I was apprehensive in introducing more ambiguity into a locus in which the individual isoform expression is a relevant information. However, it seems like the EM gave me results that are very close to what I was expecting. ...
written 5 weeks ago by elsoja70
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... I'm very sorry! I read your question wrong! I don't think that there's a method that can identify if a read is from a mRNA. I can suggest two alternatives: - If the organism that you are working with has a reference annonation, you can map the reads to the mRNA sequences (using BWA or Bowtie) and t ...
written 5 weeks ago by elsoja70
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RNA-Seq quantification of a heterozygous individual with a short deletion
... I'm quantifying transcript expression of RNA-Seq data collected from a mouse that is heterozygous in a given locus. One of the alleles is wild-type while the other has a deletion (~20bp). Should I take any special care when quantifying those samples or can I use Salmon/Kallisto/RSEM with a standard ...
rna-seq written 5 weeks ago by elsoja70 • updated 5 weeks ago by Lior Pachter460
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Comment: A: Can I filter mRNA from bulk RNA-seq reads?
... Yes. You can use SortMeRNA for that. https://bioinfo.lifl.fr/RNA/sortmerna/ ...
written 5 weeks ago by elsoja70
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Comment: C: Is it possible to detect lncRNA in a de novo assembled genome?
... There are some tools that can distinguish between lncRNAs and mRNAs even if the transcript sequence is incomplete (as you would expect in a de novo assembly). You can check Figure 5 [here][1]. [1]: https://www.biorxiv.org/content/10.1101/620880v1.full ...
written 8 weeks ago by elsoja70
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Answer: A: Currently what is the best tool for long non-coding RNA annotation? Is FEELnc a
... (Update to the thread) FEELnc is still a great choice, but some other great lncRNA annotation tools were published recently. - [RNAsamba][1] (disclaimer: I'm the author of this tool) - [lncFinder][2] - [LncADeep][3] [1]: https://rnasamba.lge.ibi.unicamp.br/ [2]: http://bmbl.sdstate.edu/lncfi ...
written 8 weeks ago by elsoja70
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Answer: A: How to extract lncRNA from CPC2 output?
... I'd suggest you not to use CPC2 because there are several better performing alternatives out there. I've developed RNAsamba, a software that has the same purpose of CPC2 with a much higher classification performance. You can use it online here: https://rnasamba.lge.ibi.unicamp.br/ As for your quest ...
written 8 weeks ago by elsoja70
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Answer: A: Software and algorithm for identification of tissue-specific express genes
... If you're looking for a database of expression patterns, including tissue-specificity, you can take a look at [PaGenBase][1]. In case you want to identify tissue-specific genes in your own data, you can use [tspex][2], a tool that I've developed. It offers a variety of tissue-specificity metrics, in ...
written 5 months ago by elsoja70
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Comment: C: How to calculate "Tissue specificity score" using JSD
... You're welcome! In the next few days I plan to release a new version with a CLI interface and a full tutorial explaining how to use the package inside Python. ...
written 6 months ago by elsoja70
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Answer: A: How to calculate "Tissue specificity score" using JSD
... In case you're still interested in that, I developed a Python package that computes several tissue-specificity metrics, including JSD. http://github.com/apcamargo/tspex I'm finishing a web version of it that will be online soon (I hope). ...
written 6 months ago by elsoja70

Latest awards to elsoja

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