User: ZheFrench
ZheFrench • 120
- Reputation:
- 120
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- Location:
- France
- Last seen:
- 2 weeks ago
- Joined:
- 3 years, 1 month ago
- Email:
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Posts by ZheFrench
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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 18 days ago by
ZheFrench • 120
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1
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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 5 weeks ago by
ZheFrench • 120
1
vote
1
answer
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1
answer
... 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 ...
written 5 weeks ago by
ZheFrench • 120
• updated
5 weeks ago by
Devon Ryan ♦ 79k
0
votes
1
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157
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1
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... Alreardy tried. No worked saying Jar is missing value from Cytoscape-App in its manifest file. ...
written 7 weeks ago by
ZheFrench • 120
0
votes
1
answer
157
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1
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... not working with cytoscape 3.6.1
Jar is downloaded from the link but not automatically installed. ...
written 7 weeks ago by
ZheFrench • 120
2
votes
1
answer
157
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1
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... 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 ...
0
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... Identify bidirectional transcripts, separe them into two different bam, to make 2 bigwigs to display distinctly depending both orientation. ...
written 8 weeks ago by
ZheFrench • 120
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0
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91
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... eRNAs are bi-directionally transcribed.
I was wondering how to separe them from a bam to make distinct bigwig using orientation and strand appartenance.
...
written 8 weeks ago by
ZheFrench • 120
1
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1
answer
160
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1
answer
... 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... ...
written 3 months ago by
ZheFrench • 120
• updated
3 months ago by
Ben_Ensembl • 600
3
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0
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204
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... 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 ...
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For Why sequence is unmapped by bwa but position is given in Sam file and also can be aligned by blat ?
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For Samtools tview : what does underlined reads mean ? Secondary or Orphan
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