User: rioualen

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rioualen400
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France
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1 month ago
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4 years, 11 months ago
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Posts by rioualen

<prev • 70 results • page 1 of 7 • next >
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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 5 weeks ago by rioualen400
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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 4 months ago by rioualen400
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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 4 months ago by rioualen400 • updated 4 months ago by Asaf8.0k
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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 5 months ago by rioualen400
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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 12 months ago by rioualen400
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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 12 months ago by rioualen400
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Comment: C: Building sequence logo from uneven sequences
... Yeah but I'm afraid of losing information, and there has to be a cleaner way to do it, it seems like quite a basic problem to me... ...
written 12 months ago by rioualen400
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Comment: C: Building sequence logo from uneven sequences
... Yeah that's the idea, only I don't want the "N" to appear, for it kinda disturbs the visualization! ...
written 12 months ago by rioualen400
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Comment: C: Building sequence logo from uneven sequences
... The second one I posted is from weblogo, but maybe I'm missing some parameter here? I just posted 5 sequences here but they're 52 in this particular case. ...
written 12 months ago by rioualen400
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Building sequence logo from uneven sequences
... Hi, I'm looking for methods to build logo from fasta sequences. I'm not sure what strategy to adopt. My input is a fasta file containing various sequences of various sizes (precisely binding sites, so they're rather short). Looks like this: >Chromosome:180614-180629 GTAAATTACCGTCAG ...
fasta weblogo ggseqlogo alignment logo written 12 months ago by rioualen400

Latest awards to rioualen

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For C: Get chromosome sizes from fasta file
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Get chromosome sizes from fasta file
Popular Question 5 weeks 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 6 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 12 months ago, asked a question that was upvoted at least 5 times. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 12 months ago, created a question with more than 1,000 views. For Get chromosome name from RefSeq format for C.elegans
Popular Question 12 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 13 months ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Popular Question 13 months ago, created a question with more than 1,000 views. For Get chromosome name from RefSeq format for C.elegans
Popular Question 13 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 14 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 14 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 14 months ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Pundit 19 months ago, created a comment with more than 10 votes. For C: Get chromosome sizes from fasta file
Epic Question 19 months ago, created a question with more than 10,000 views. For Get chromosome sizes from fasta file
Popular Question 19 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 2.2 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 2.5 years ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Great Question 2.5 years ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Student 2.5 years ago, asked a question with at least 3 up-votes. For Get chromosome sizes from fasta file
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Get chromosome sizes from fasta file
Scholar 2.8 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans

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