User: ZheFrench

gravatar for ZheFrench
ZheFrench70
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70
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France
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1 day, 11 hours ago
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2 years, 8 months ago
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Posts by ZheFrench

<prev • 33 results • page 1 of 4 • next >
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Use PWM from CISBP-rna to find motif with MEME (FIMO)
... MEME need a specific matrix for input. The software gives a list of utilities for conversion matrix. For example, you can convert jaspar PFM to MEME matrix input to use with FIMO and find motifs in a sequence. CISBP-rna [http://cisbp-rna.ccbr.utoronto.ca/][1] let access a list of PWM matrices but I ...
cisbp meme motif written 3 days ago by ZheFrench70
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Comment: C: Trim galore terminates with exit signal: '256'
... Yeah this is what I did fastq's from ENA solution and it then worked fine. Thanks ...
written 6 days ago by ZheFrench70
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Comment: A: Trim galore terminates with exit signal: '256'
... I got the same issue after a download on sra: fastq-dump -split-3 SRR4235527 trim_galore --paired --fastqc --output_dir /GM12878/ SRR4235527_R1.fastq SRR4235527_R2.fastq > cutadapt: error: At line 3: Sequence descriptions in the FASTQ file > don't match ('SRR4235527.43679310 TUPAC_0 ...
written 7 days ago by ZheFrench70
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Salmon and reads order in fastq in quasi-mapping-based mode
... Really a naïve question but it's a little while I have this one in mind. From Salmon doc : *"If your reads or alignments do not appear in a random order with respect to the target transcripts, please randomize / shuffle them before performing quantification with Salmon."* I don't understand if th ...
salmon written 8 days ago by ZheFrench70 • updated 8 days ago by ATPoint2.6k
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Access old version of ensembl via rest API
... How do you access old version of ensembl database via rest ? Server adress is https://rest.ensembl.org but is there an alternative as http://rest.jul2016.archive.ensembl.org/ for the version you want to work on or do you have to set database version in the parameter send ? If so could you provide ...
ensembl written 11 days ago by ZheFrench70 • updated 11 days ago by Emily_Ensembl14k
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Comment: C: Jbrowse install via conda, how do you launch it ?
... yeah I succeed to make it work finally ...doing a symlink to a /var/www, and following the same link you send me tks ...
written 4 weeks ago by ZheFrench70
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Jbrowse install via conda, how do you launch it ?
... Naïve question but once you have done : > conda install jbrowse and that install worked perfectly well. How do you use/access jbrowse then ? ...
conda jbrowse written 4 weeks ago by ZheFrench70
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Comment: C: How Do you find constitutive exons in Ensembl or UCSC
... Thanks by the way for your input ! ...
written 10 weeks ago by ZheFrench70
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Comment: C: How Do you find constitutive exons in Ensembl or UCSC
... My PI does :) .Yeah I do understand and I'm totally agreed in fact. That's really depending on annotations you look at. In UCSC, gencode 24 is displayed for annotation and it seems exon(35/37) is alternative but all the others seems constitutive. When you look gtf imported from Gencode 25 based on E ...
written 10 weeks ago by ZheFrench70
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How Do you find constitutive exons in Ensembl or UCSC
... How do you find exons annotated as constitutive from official source Ensembl or UCSC? I first tried BioMart using Exon Information : Constitutive Exon. But that didn't give me what I expected. All exons are most of the time annotated as 0 meaning alternative whereas the most part of them should be ...
ensembl biomart exons constituve ucsc written 10 weeks ago by ZheFrench70 • updated 10 weeks ago by Pierre Lindenbaum102k

Latest awards to ZheFrench

Supporter 6 days ago, voted at least 25 times.
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Popular Question 9 months ago, created a question with more than 1,000 views. For Samtools tview : what does underlined reads mean ? Secondary or Orphan

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