Daniel Gautheret
@DGautheret
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Bioinformatics, RNA, Genomics @univparissaclay & @GustaveRoussy.
Ile-de-France, France
Joined April 2017
👇👇.
Are you worried about your DNA revealing too much about you? The @washingtonpost says you should be very worried. I have a different take:
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Now indexing over 10k RNA-seq samples with accurate counts!.
REINDEER2: practical abundance index at scale #biorxiv_bioinfo.
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Generate videos in just a few seconds. Try Grok Imagine, free for a limited time.
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My new starter pack for students entering the k-mer world!.
Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics:
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RT @RayanChikhi: Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics:
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RT @MolecularCell: Modulation of protein activity by small RNA base pairing internal to coding sequences https://t.….
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RT @RayanChikhi: We have updated all Logan contigs, now at version 1.1! Contiguity has been much improved (2x) and a duplicated k-mers bug….
github.com
Logan Unitigs and Contigs. Contribute to IndexThePlanet/Logan development by creating an account on GitHub.
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Dear young investigator in cancer bioinformatics: check our postdoc position on reference-free, organ agnostic transcriptome signatures of cancer at I2BC, Gif sur Yvette.
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Anyway I find Logan search super exciting. I think it is more powerful and practical from a biologist's standpoint than previous large scale SRA search tools.
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Ouch after a few more tests I have reached my query limit. I need to wait 7h. I should have selected the whole database for search, because now I want to query other sample types (DNA, meta transcriptomics etc.).
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Anyway, when tissue was available, it was almost always prostate or prostate cancers. That tells me there are not many false positives. A few exceptions (mammary, urothelial) would be worth exploring. I tested Unitig retrieval. Works fine. It even gives counts, yeah!.
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The table view contains a selection of SRA data fields, including "tissue", which was the most interesting to me. Unfortunately, SRA meta-data is terrible. ~75% of samples have no tissue information. This is not Logan's fault.
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The output came as advertised in a few minutes. I got 2600 hits overall. That is more samples with TMPRSS2-ERG fusions than in the whole Cosmic database (2300). Wonderful! Although probably a good part are from the same few cancer cell lines.
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"probes" are short sequence selected around an event of interest, that contain only 31-mers that overlap the event. Logan search only allows one query at a time, so I did 3 queries, selecting the human RNA-seq group. That should be 1 or 2 millions datasets.
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I wanted to find human RNA samples expressing the TMPRSS2-ERG fusion found in 1/3 of prostate cancers. I used 3 TMPRSS2-ERG fusion probes from the Reindeer use-cases repo
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So here is some feedback on my first tests with Logan Search. 🧵.
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RT @I2BCParisSaclay: Reference-free exploration of cancer RNA datasets | @scoopit
scoop.it
Bioinformaticians finds new ways to analyze cancer RNA in very large datasets Cancer cells produce an immense diversity of RNA molecules. Using deep sequencing technologies, scientists explore these...
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RT @anne__lopes: very happy to present our latest work on the diversity of RiboSeq signals associated with canonical and noncanonical trans….
genomebiology.biomedcentral.com
Background Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their...
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