User: ZheFrench

gravatar for ZheFrench
ZheFrench140
Reputation:
140
Status:
Trusted
Location:
France
Last seen:
1 day, 4 hours ago
Joined:
3 years, 7 months ago
Email:
j*********@gmail.com

Posts by ZheFrench

<prev • 53 results • page 1 of 6 • next >
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FastQ ColorSpace to BaseSpace format in 2018
... Nowadays, is there a good way to convert colorSpace fastq from ABI platform to base space format ? Or at least, to align them in bam and maybe then you can extract to base space fastq ... I'm used to work with STAR for alignment but it's not designed to align colorspace fastq(same for bowtie2)...s ...
colorbase written 3 days ago by ZheFrench140 • updated 3 days ago by Antonio R. Franco3.9k
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How to visualise/explore Hi-C maps per chromosome at 100Kb and 40Kb
... From here[enter link description here][1] I can download Hic maps per chromosome at 100kb and 40 kb . I have no expertise with Hic data. I was wondering how to exploit these files which extension is ."abc". I'd like to have coordinates in text file with regions of interaction and strength/statistics ...
hic written 7 days ago by ZheFrench140 • updated 6 days ago by Alex Reynolds26k
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BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
... I am wondering what is the difference between this two reference package in R ? hg38 and GRCh38 should be same sequence assembly, right ? So what the point of creating this two reference package to access raw sequence. ...
genome R version assembly written 6 weeks ago by ZheFrench140 • updated 26 days ago by igor6.9k
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Comment: C: DESEQ2 size factors change when number of samples change in the design
... Ok I got it , but do you know how is it computed ? ...
written 7 weeks ago by ZheFrench140
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DESEQ2 size factors change when number of samples change in the design
... For example, when you analyse Untreated condition vs Day1Treatment condition with only these samples in your design you will get some size factors. If you have also set up a Day6Treatment condition in your design (but you don't use it yet), and want to to do the same comparison Untreated vs Day1Tre ...
deseq2 written 7 weeks ago by ZheFrench140
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Heatmap with normalised count from DESEQ2
... I was wondering which is better (or if one of this method is wrong ) for plotting in a heatmap normalised count from deseq2 : `counts(dds,normalized=TRUE)` : z-score( log2(norm count +1) ), z-score(norm count ) or just log2(norm count +1) ...
deseq2 heatmap written 7 weeks ago by ZheFrench140 • updated 7 weeks ago by Kristin Muench330
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Comment: C: How to define Basal B subtype from TCGA breast cancer patient samples ?
... Yeah that was my first idea. By the way how do you scaled TPM values ? ...
written 3 months ago by ZheFrench140
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How to define Basal B subtype from TCGA breast cancer patient samples ?
... TCGA provide a molecular classification (Luminal A , Luminal B, Basal, Normal like, HER2 enriched) Basal subtype can be divided in basal A and basal B. (Kao et al., 2009; Neve et al., 2006) It has been done using expression from MicroArray via Significance Analysis of Microarrays (SAM) or PAM using ...
tcga cancer written 3 months ago by ZheFrench140
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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 6 months ago by ZheFrench140
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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 7 months ago by ZheFrench140

Latest awards to ZheFrench

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 8 months ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 9 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Supporter 11 months ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 18 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 20 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 20 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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