User: ZheFrench

gravatar for ZheFrench
ZheFrench110
Reputation:
110
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Trusted
Location:
France
Last seen:
1 week, 3 days ago
Joined:
2 years, 10 months ago
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j*********@gmail.com

Posts by ZheFrench

<prev • 36 results • page 1 of 4 • next >
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TSS coordinates from Ensembl Biomart
... When you use biomart you can get 1-based TSS start coordinate. If you want to transform this coordinate to 0-based format you need to remove 1, whatever the strand is , right ? If strand + , TSS is chr11 48488717 coordinate in biomart. If you want bed format, it will be : > chr11 48488716 4 ...
ensembl biomart written 21 days ago by ZheFrench110
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Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
... I was wondering how to Estimate Fragment Size from bamfile directly in my code using some libraries cited in title . Some functions might already exists somewhere I suppose...Peak caller MACS does that. (d value) but I'd like to reproduce it by myself. ...
htseq deeptools pysam written 25 days ago by ZheFrench110
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How to get flanking intron sizes for genomic exon coordinates ?
... Before going to make some script, i'm asking if someone does have something ? using gtf or a flattened exon list. I think that must easily achieve using bedtools and some line of codes... But it's the end of year so I'm feeling lazy :) ...
gtf annotation written 7 weeks ago by ZheFrench110
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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 10 weeks ago by ZheFrench110
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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 11 weeks ago by ZheFrench110
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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 11 weeks ago by ZheFrench110
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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 11 weeks ago by ZheFrench110 • updated 11 weeks ago by ATPoint3.0k
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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 weeks ago by ZheFrench110 • updated 11 weeks 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 3 months ago by ZheFrench110
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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 3 months ago by ZheFrench110

Latest awards to ZheFrench

Popular Question 21 days ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Supporter 11 weeks ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 9 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 11 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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