User: ZheFrench
ZheFrench • 140
- 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
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... 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 ...
written 3 days ago by
ZheFrench • 140
• updated
3 days ago by
Antonio R. Franco • 3.9k
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... 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 ...
written 7 days ago by
ZheFrench • 140
• updated
6 days ago by
Alex Reynolds ♦ 26k
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... 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. ...
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... Ok I got it , but do you know how is it computed ? ...
written 7 weeks ago by
ZheFrench • 140
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... 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 ...
written 7 weeks ago by
ZheFrench • 140
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... 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) ...
written 7 weeks ago by
ZheFrench • 140
• updated
7 weeks ago by
Kristin Muench • 330
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... Yeah that was my first idea. By the way how do you scaled TPM values ? ...
written 3 months ago by
ZheFrench • 140
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... 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 ...
written 3 months ago by
ZheFrench • 140
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... 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
ZheFrench • 140
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... 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
ZheFrench • 140
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