User: antoinefelden

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3 years, 11 months ago
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Posts by antoinefelden

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Batch Entrez outputs nothing
... I'm wanting to retrieve taxonomy info from UIDs - which EntrezDirect looks like it's doing! Thanks! `esearch -db "nucleotide" -query "MG737737.1"` gives me the record, and I can then pipe it into `efetch` (using one UID as an example). The output is pretty large, any pointer about how to parse the o ...
written 29 days ago by antoinefelden30
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Comment: C: Batch Entrez outputs nothing
... If I try with Firefox, the tab name becomes "Error - Nucleotide - NCBI", so there is something wrong going on... (see screenshot https://ibb.co/b78Yd3Y) Still under investigation! ...
written 4 weeks ago by antoinefelden30
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Comment: C: Batch Entrez outputs nothing
... Ok, weird, I am also able to click "Retrieve records for 10 UID(s)" link, but then the page is empty... https://ibb.co/RNRTbh7 ...
written 4 weeks ago by antoinefelden30
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Batch Entrez outputs nothing
... Hi, I'm trying to use Batch Entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez) to look up the identifiers below, but although UID are recognised (and return records in the CBI database) - the output is empty. Any idea why? Thanks! Reproducible example (to copy paste in a .txt document): ...
ncbi batch entrez written 4 weeks ago by antoinefelden30 • updated 29 days ago by genomax91k
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How to interpret Q2 values in Partial Least Square analysis?
... I'm having problem interpreting the output of perf(PLS), and I could not find any case to relate to in the MixOmics documentation. My dataset is quite small, I want to relate a 12x160 matrix (expression values for 160 immune genes in 12 samples) with a 12x11 matrix (viral loads for 11 viruses in th ...
mixomics pls written 2.0 years ago by antoinefelden30
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Answer: A: How to deal with single transcripts assigned to multiple genes?
... Okay, I solved that problem, which was not really one but in fact a feature of StringTie. See https://github.com/gpertea/stringtie/issues/170 In a nutshell, there is an alternative - simpler - StringTie pipeline that skip the assembly step. So what this does is simply to map the reads, without loo ...
written 2.1 years ago by antoinefelden30
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Is it okay to remove uncharacterised transcripts from downstream analysis in RNA-seq?
... I work with a reference genome that is only partially annotated, and I'm wondering if it's okay for me to discard uncharacterised genes from my dataset (once I've properly calculated TMM-normalisation factors from all transcripts, including the uncharacterised ones). I can deal with having lots of ...
wgcna rna-seq dge written 2.1 years ago by antoinefelden30 • updated 21 months ago by h.mon31k
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How to deal with single transcripts assigned to multiple genes?
... After I ran StringTie after Hisat2 on a non-model RNA-seq data set (i.e. Argentine ant), I realised that some StringTie transcripts were assigned to multiple genes (see exemple below) which is causing many problems down the line. 24887 MSTRG.1473 LOC105670921 24920 MSTRG.1473 LOC1056707 ...
stringtie rna-seq hisat2 written 2.1 years ago by antoinefelden30 • updated 2.1 years ago by RamRS30k
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Comment: C: Is it valid to compare the expression of pre-defined candidate genes from RNA-se
... A bit of background: I work on a non-model organism - the Argentine ant - that does have a sequenced genome but limited annotation, and no actual functional characterisation. Which is why I try to look at the big picture as much as I can, because not much is known in the genes that turned out to be ...
written 2.9 years ago by antoinefelden30
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Answer: A: Is it valid to compare the expression of pre-defined candidate genes from RNA-se
... To be specific, I'm trying to investigate if immune genes show condition-specific expression profiles. I first produced heatmaps with a set of immune genes that do show consistent differences between conditions across replicates. Then, I did a simple `glm(scale(log2(TMMs))~condition)` that showed si ...
written 2.9 years ago by antoinefelden30

Latest awards to antoinefelden

Popular Question 19 months ago, created a question with more than 1,000 views. For Target fragment size versus final insert size
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How to deal with single transcripts assigned to multiple genes?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Target fragment size versus final insert size
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to deal with single transcripts assigned to multiple genes?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Target fragment size versus final insert size

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