User: rioualen

gravatar for rioualen
rioualen470
Reputation:
470
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Trusted
Location:
France
Last seen:
1 day, 19 hours ago
Joined:
5 years, 5 months ago
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Posts by rioualen

<prev • 74 results • page 1 of 8 • next >
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Answer: A: can't run Aracne -- Java error
... I tried running Aracne (sourceforge version) on my old laptop and it worked just fine (Ubuntu 16.04 + openjdk 1.8.92). So in my macbook I created a conda environment, installed an old Java version in there (opendjdk 8.0.192) and Aracne is running fine. ...
written 5 months ago by rioualen470
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Comment: C: can't run Aracne -- Java error
... I get that: `Cannot find file "usage.txt"! Please make sure it is in the current working directory.` ...
written 5 months ago by rioualen470
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Comment: C: can't run Aracne -- Java error
... The `bash` command gets me a `aracne2.macosx: aracne2.macosx: cannot execute binary file` error. And when trying to open outside of the terminal macos does not know which application to execute it with ...
written 5 months ago by rioualen470
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can't run Aracne -- Java error
... Hello, I'm trying to run Aracne in order to generate network data from expression data. I can't seem to run the program, despite trying different versions: - I downloaded the MacOS file from there http://califano.c2b2.columbia.edu/aracne but I don't know how to use the .macosx file - I downloade ...
network rna-seq aracne written 5 months ago by rioualen470
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Bedtools genomecov option to keep columns 4-6?
... Hi, I'm using `bedtools genomecov` in order to get the coverage from one bedfile either with option -d (coverage per position) or -bga (bedgraph output). However my input bedfile comes in 6-column format, and the last 3 are not reported in the output files. I'd be particularly interested in keeping ...
genomecov bed bedtools written 7 months ago by rioualen470
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Comment: C: Generate sequence alignment and heatmap for TF binding sites
... Yeah I know it, but I'm not looking to produce the logo, I'm rather interested in how the sequences possibly cluster into subgroups, or if they're more like a continuum. ...
written 10 months ago by rioualen470
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Generate sequence alignment and heatmap for TF binding sites
... Hi, I'm looking for programs to generate heatmaps from DNA sequences (TF binding sites) and clusterize them. I like this type of figure but it's from a Matlab library, and I haven't found equivalents in R or else. Any suggestions? Thanks a lot! ![Figure][1] [1]: https://i.postimg.cc/mgDXfMRQ/Sc ...
alignment chip-seq logo heatmap written 10 months ago by rioualen470 • updated 10 months ago by Asaf8.5k
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Comment: C: Modern software for whole genome alignment visualization
... Hi, any update about this? I'm also looking for a sorta genome browser to visualize whole-genome alignments for bacterial genomes, but I can't seem to make any of the tools mentioned here work -- many of which seem not to be maintained anymore... ...
written 11 months ago by rioualen470
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Comment: C: Building sequence logo from uneven sequences
... >ECK120011216(+) ----GTAAATTACCGTCAG----- >ECK120011212(+) ----GTAAAGACGAACAATAAAT- >ECK120016885(+) ----ACAATAAATTTTTAC----- >ECK120017106(+) ----GTAAAACCTGGTAAG----- >ECK120016896(+) ----GTAAAGAGATCACCA----- >ECK120016894(+) ----GTA ...
written 19 months ago by rioualen470
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Comment: C: Building sequence logo from uneven sequences
... Apart from the apparent gaps that it generates, it also introduces a bias in the evaluation of nucleotide weights, and impacts the visualisation: ![enter image description here][1] ![enter image description here][2] [1]: https://i.imgur.com/xWaVxYb.png [2]: https://i.imgur.com/vhScWBf.png ...
written 19 months ago by rioualen470

Latest awards to rioualen

Appreciated 5 months ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Great Question 5 months ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Popular Question 5 months ago, created a question with more than 1,000 views. For Get chromosome name from RefSeq format for C.elegans
Scholar 5 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: can't run Aracne -- Java error
Scholar 7 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For C: Get chromosome sizes from fasta file
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Get chromosome sizes from fasta file
Popular Question 7 months ago, created a question with more than 1,000 views. For Is there a simple way to get the max coverage of a bedgraph file in python?
Popular Question 13 months ago, created a question with more than 1,000 views. For Is there a simple way to get the max coverage of a bedgraph file in python?
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 19 months ago, created a question with more than 1,000 views. For Get chromosome name from RefSeq format for C.elegans
Popular Question 19 months ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Appreciated 19 months ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Popular Question 20 months ago, created a question with more than 1,000 views. For Get chromosome name from RefSeq format for C.elegans
Popular Question 20 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 21 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 21 months ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Great Question 21 months ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Pundit 2.2 years ago, created a comment with more than 10 votes. For C: Get chromosome sizes from fasta file
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Get chromosome sizes from fasta file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Appreciated 3.0 years ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file

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