User: Corentin

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Corentin100
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Posts by Corentin

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Comment: C: Pilon polish draft assembly, but it didn't work
... If you have time you can try to map with the -M option only, and then with the -P option only, to see which one of the two (or the two together) is causing the issue. I remember that for pilon the bams need to be "sorted in coordinate order and indexed" (https://github.com/broadinstitute/pilon/wiki ...
written 1 day ago by Corentin100
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Comment: C: Pilon polish draft assembly, but it didn't work
... Hi, did you checked your bam file ? You can run "samtools flagstat" on it to check the number of reads mapped to the reference. ...
written 7 days ago by Corentin100
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Answer: A: Selecting fastq sequences
... Hi, Your barcode variable is a *file object* and so an *iterator* (source: https://docs.python.org/2/library/stdtypes.html#bltin-file-objects **A file object is its own iterator** and https://stackoverflow.com/questions/16994552/is-file-object-in-python-an-iterable), when you loop through a file ob ...
written 10 days ago by Corentin100
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Answer: A: Data for drawing Heatmaps (RNA-seq)
... Hi, The normalization should be performed by the tool you are using (the most popular being EdgeR, DESeq2 and limma), each one of them has a different way of normalizing the data, but if your data is robust (one of the important thing is having enough replicates), they should give similar results, ...
written 6 weeks ago by Corentin100
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Comment: C: Help! How to plot RNASeq data in PCA
... As an alternative to PCA you can also try MDS plots : https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/plotMDS.DGEList but it should give similar results ...
written 10 weeks ago by Corentin100
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Answer: A: expression to networking
... If you have access to the enzyme annotations for your genes, you can use the KEGG API which can link enzymes to kegg pathways (http://www.kegg.jp/kegg/rest/keggapi.html). You can use R (or your favorite language) to access the API. The file to link enzymes and pathways is available here : http://re ...
written 3 months ago by Corentin100
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Answer: A: CNV detection techniques, algorithms, applications ...
... Hi, There are already a few tools out there for CNV detection: [https://omictools.com/cnv-detection2-category][1] . They are often specialised in Exome sequence data. You can take a look at how they work. Their implementation is described in the associated paper (when there is one). I know that ...
written 7 months ago by Corentin100
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Comment: C: RSEM: identical expression for different cufflinks transcripts
... Thank you for your answer, I had a look with IGV and these transcripts are indeed overlapping isoforms (they are almost the same). ...
written 7 months ago by Corentin100
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RSEM: identical expression for different cufflinks transcripts
... Hi, I ran the tuxedo pipeline on rna seq data. And I used RSEM/limma for the differential expression analysis. I noticed something peculiar in the counts matrix from RSEM, some transcripts have exactly the same expression level for all the samples: "TCONS_00086761" 46.23 46.23 61.4 ...
cufflinks rna-seq expression written 7 months ago by Corentin100

Latest awards to Corentin

Appreciated 10 days ago, created a post with more than 5 votes. For A: Selecting fastq sequences
Scholar 10 days ago, created an answer that has been accepted. For A: expression to networking
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: expression to networking
Scholar 3 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: expression to networking

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