User: endrebak
endrebak • 570
- Reputation:
- 570
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- https://github.com/end...
- Last seen:
- 3 weeks, 1 day ago
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- 1 year, 2 months ago
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Posts by endrebak
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Comment:
C: generate fastq with bed file
... That generates a fasta, not a fastq :) ...
written 9 weeks ago by
endrebak • 570
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... Snakemake all the things ...
written 12 weeks ago by
endrebak • 570
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... Thanks, changed my answer :) ...
written 6 months ago by
endrebak • 570
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... If you want to discuss bam-support, please do it here: https://github.com/endrebak/epic/issues/44
...
written 8 months ago by
endrebak • 570
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... You can scroll down Istvan 🙂 ...
written 8 months ago by
endrebak • 570
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... You will probably rerun the analyses many times. Having to run a time-consuming conversion step (the most time-consuming one in the algorithm) each time would be silly. It is also IO-intensive so parallell execution would not help much.
I am not just writing epic but a lot of helper scripts for ChI ...
written 8 months ago by
endrebak • 570
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Comment:
C: Create bigwigs in python?
... It seems like bw.addEntries would take four enormous lists if I know all the entries upfront. I guess I should chunk the data and add a 1000 entries at a time... ...
written 8 months ago by
endrebak • 570
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1
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379
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Comment:
C: Create bigwigs in python?
... Wonderful, thanks for your effort! Python3 even <3 ...
written 8 months ago by
endrebak • 570
3
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1
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... I want to create bigwigs in Python. Is there a library that can do this?
Two ways of doing it that I'd rather avoid:
Currently I use rpy2 with rtracklayer and genomicranges through bioconda. This works, but is a bit heavy on the dependencies. Example code:
https://github.com/endrebak/epic/blob/25 ...
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... If you only have one metadata column and you would like to keep it, this modification of Devon Ryan's answer works:
df <- data.frame(seqnames=seqnames(gr),
starts=start(gr)-1,
ends=end(gr),
names=c(rep(".", length(gr))),
scores=elementMetadata(gr)[,1],
strands=strand(gr)
...
written 9 months ago by
endrebak • 570
Latest awards to endrebak
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For epic: new ChIP-Seq caller based on the SICER algorithm
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: How To Convert Gencode Gtf Into Bed Format ?
Voter
9 months ago,
voted more than 100 times.
Student
10 months ago,
asked a question with at least 3 up-votes.
For I want to store a docker image reproducing a paper. Is there a host for docker images of studies?
Scholar
10 months ago,
created an answer that has been accepted.
For A: Given a link that displays genome browser data, how do I download a pdf using a
Student
10 months ago,
asked a question with at least 3 up-votes.
For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
Supporter
13 months ago,
voted at least 25 times.
Appreciated
14 months ago,
created a post with more than 5 votes.
For epic: new ChIP-Seq caller based on the SICER algorithm
Autobiographer
14 months ago,
has more than 80 characters in the information field of the user's profile.
Appreciated
15 months ago,
created a post with more than 5 votes.
For epic: new ChIP-Seq caller based on the SICER algorithm
Student
15 months ago,
asked a question with at least 3 up-votes.
For epic: new ChIP-Seq caller based on the SICER algorithm
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