User: rioualen

gravatar for rioualen
rioualen360
Reputation:
360
Status:
Trusted
Location:
France
Last seen:
5 days, 13 hours ago
Joined:
3 years, 10 months ago
Email:
r*************@gmail.com

Posts by rioualen

<prev • 66 results • page 1 of 7 • next >
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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 5 days ago by rioualen360
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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 5 days ago by rioualen360
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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 6 days ago by rioualen360
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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 6 days ago by rioualen360
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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 6 days ago by rioualen360
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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 6 days ago by rioualen360
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Comment: C: Trimming adapter sequences - is it necessary?
... Bowtie2 for example has an additional option to perform local alignments like this (not a default option) ![][1] I think Subread-align works this way as well, but I don't know about other mapping programs. [1]: https://i.imgur.com/hP8ozV7.png ...
written 7 weeks ago by rioualen360
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Comment: C: Trimming adapter sequences - is it necessary?
... Sorry for digging out such an old debate, but I was thinking maybe performing a local alignment would replace the trimming of the reads, be it the quality trimming or trimming adapters. Does it make sense? Thank you for any input. ...
written 7 weeks ago by rioualen360
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Comment: C: Download data from GEO/SRA using link
... I didn't know this tool, it does just the job! Thanks a lot. ...
written 10 weeks ago by rioualen360
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Download data from GEO/SRA using link
... I can't seem to find an easy way to download raw data from GEO. Say I want these experiments: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93506 There used to be links to download SRA files, but I can't find it anymore. The best i can do is to go to each and every sample page, get the SRX ...
geo sra fastq written 10 weeks ago by rioualen360 • updated 10 weeks ago by genomax68k

Latest awards to rioualen

Appreciated 15 days ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Popular Question 26 days ago, created a question with more than 1,000 views. For Get chromosome name from RefSeq format for C.elegans
Popular Question 26 days ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 7 weeks 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 9 weeks ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Pundit 7 months ago, created a comment with more than 10 votes. For C: Get chromosome sizes from fasta file
Epic Question 7 months ago, created a question with more than 10,000 views. For Get chromosome sizes from fasta file
Popular Question 7 months ago, created a question with more than 1,000 views. For Merge bed files, keep the peak count
Popular Question 12 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
Appreciated 17 months ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Great Question 17 months ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Popular Question 17 months 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 17 months ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Student 17 months ago, asked a question with at least 3 up-votes. For Get chromosome sizes from fasta file
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Get chromosome sizes from fasta file
Scholar 21 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Student 2.2 years ago, asked a question with at least 3 up-votes. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Scholar 3.4 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Scholar 3.9 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans

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