User: ZheFrench

gravatar for ZheFrench
ZheFrench120
Reputation:
120
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Trusted
Location:
France
Last seen:
2 weeks ago
Joined:
3 years, 1 month ago
Email:
j*********@gmail.com

Posts by ZheFrench

<prev • 45 results • page 1 of 5 • next >
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Answer: A: ATAC-seq peak calling with MACS
... So finally what is the consensus to use for MACS2 with ATAC-SEQ paired-end ? I read that -f BAMPE was a good pratice . But then should it be used with --nomodel option ? For what it worth, this is what I'm using until now on my bam without duplicates: macs2 callpeak --verbose 3 --treatment m ...
written 18 days ago by ZheFrench120
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Comment: C: Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
... Humm strange... conda remove deeptools Solving environment: done ## Package Plan ## removed specs: - deeptools The following packages will be REMOVED: deeptools: 2.5.7-py35_0 bioconda Proceed ([y]/n)? y Preparing transactio ...
written 5 weeks ago by ZheFrench120
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Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
... Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie ~$ conda update deeptools Solving environment: done # All requested packages already installed. ~$ conda install -c bioconda deeptools Solving environment: done # All requested packages alre ...
deeptools written 5 weeks ago by ZheFrench120 • updated 5 weeks ago by Devon Ryan79k
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Comment: C: Cytoscape : how to color same nodes with several colors ?
... Alreardy tried. No worked saying Jar is missing value from Cytoscape-App in its manifest file. ...
written 7 weeks ago by ZheFrench120
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Comment: C: Cytoscape : how to color same nodes with several colors ?
... not working with cytoscape 3.6.1 Jar is downloaded from the link but not automatically installed. ...
written 7 weeks ago by ZheFrench120
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Cytoscape : how to color same nodes with several colors ?
... Cytoscape : how to color same nodes with several colors ? An example [here][1] in figure E : [1]: https://www.ncbi.nlm.nih.gov/pubmed/27863249 ...
cytoscape written 7 weeks ago by ZheFrench120 • updated 6 weeks ago by scooter20
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Comment: C: How to separe eRNA by orientation from with GRO-SEQ data
... Identify bidirectional transcripts, separe them into two different bam, to make 2 bigwigs to display distinctly depending both orientation. ...
written 8 weeks ago by ZheFrench120
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How to separe eRNA by orientation from with GRO-SEQ data
... eRNAs are bi-directionally transcribed. I was wondering how to separe them from a bam to make distinct bigwig using orientation and strand appartenance. ...
gro-seq erna written 8 weeks ago by ZheFrench120
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How to get Transcription End site (TES) via ensembl biomart ?
... Via Biomart you can get TSS coordinates, but I don't see how you can retrieve the TES . I am certainly missing something in biomart... ...
ensembl biomart written 3 months ago by ZheFrench120 • updated 3 months ago by Ben_Ensembl600
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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 3 months ago by ZheFrench120 • updated 11 weeks ago by Biostar ♦♦ 20

Latest awards to ZheFrench

Student 12 weeks ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 3 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Supporter 5 months ago, voted at least 25 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 12 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 14 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 14 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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