User: sacha

gravatar for sacha
sacha780
Reputation:
780
Status:
Trusted
Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
2 days, 20 hours ago
Joined:
2 years, 4 months ago
Email:
s****@labsquare.org

Posts by sacha

<prev • 181 results • page 1 of 19 • next >
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Answer: A: faidx implementation with C++
... with the following fasta file : >chr1 ACGTATATATATGTAT ACGTATATATATATAT >chr2 ACGTATATATTATATT ACTATATATATTATAT ACTATATATATATATT GTATATATAAATTATA the faidx file contains : chr1 32 6 16 17 chr2 64 46 16 17 One ...
written 2 days ago by sacha780
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Localize the variant from the Crispr embryon editing paper
... I m just reading the famous paper [Correction of a pathogenic gene mutation in human embryos][1] published recently. I m trying to localize the deletion corrected on IGV or other genom browser. In the paper, they said : by a heterozygous dominant 4-bp GAGT deletion (g.9836_9839 del.,NC_00 ...
indel mybpc3 snp localize written 15 days ago by sacha780
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Comment: C: Fastq Files From Different Flowcells
... Is processing Lane separately faster than using bwa on the merged fastq file with thread option ? Which one is faster ? Strategy A or B ? I think those strategies are equivalent. Strategy A : Makefile bwa lane1.fastq bwa lane2.fastq bwa lane3.fastq bwa lane4.f ...
written 7 weeks ago by sacha780
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Tool: CutePeaks : A Sanger Trace file viewer
... We just released the first version of CutePeaks. A simple Trace file viewer written in [Qt/C++][1] under GPL3 license. It's avaible at https://github.com/labsquare/CutePeaks . There is a binary AppImage for Linux. So you can download it and run it directly. Few features for now. But we are ...
trace tool sanger scf ab1 viewer written 8 weeks ago by sacha780
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Comment: C: How to plot venn diagram from vcf-compare output ?
... yes... but I m lazzy :D ! ...
written 8 weeks ago by sacha780
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How to plot venn diagram from vcf-compare output ?
... i get the following output from vcf-compare by comparing two VCF : VN 2172 NA12878/intersect2.vcf.gz (6.8%) VN 29648 Coriell.varscan.snp.vcf.gz (20.7%) NA12878/intersect2.vcf.gz (93.2%) VN 113680 Coriell.varscan.snp.vcf.gz (79.3%) I would like to plot a Venn ...
venn vcf-compare plot written 8 weeks ago by sacha780 • updated 8 weeks ago by WouterDeCoster20k
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Answer: A: REST API to run pipeline ( not Galaxy)
... Here is a better list : https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems ...
written 3 months ago by sacha780
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Answer: A: REST API to run pipeline ( not Galaxy)
... some galaxy alternative https://seqware.github.io/ http://archive.broadinstitute.org/cancer/cga/Firehose http://bcbio-nextgen.readthedocs.io/en/latest/ http://www.taverna.org.uk/ http://rundeck.org/#LearnMore ...
written 3 months ago by sacha780
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Comment: C: MiSeq reagent kit version 3 : bad reads qualities
... Flash try to align the overloap between the forward and the reverse. If the alignement score is too low, the read is ignored. Here is the output of flash trying to merge a pairs of fastq. Do you have any suggestion for another tools ? I already tested vsearch and illumina-utils. But both had worst r ...
written 3 months ago by sacha780
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Comment: C: MiSeq reagent kit version 3 : bad reads qualities
... I updated my merged plot. It was after low qualities filtering. Now the plot shows merged just after Flash ...
written 3 months ago by sacha780

Latest awards to sacha

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Scholar 3 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 4 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 4 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Epic Question 5 months ago, created a question with more than 10,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 7 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Appreciated 8 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Appreciated 9 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Scholar 9 months ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Plotting SNP density along a chromosome from VCF files
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Scholar 10 months ago, created an answer that has been accepted. For A: bcftools extract data
Great Question 11 months ago, created a question with more than 5,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Centurion 12 months ago, created 100 posts.
Scholar 12 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 12 months ago, created an answer that has been accepted. For A: bcftools extract data
Supporter 13 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 17 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 17 months ago, created a post with more than 5 votes. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 17 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 20 months ago, created a question with more than 1,000 views. For How bcftools isec works ?
Appreciated 20 months ago, created a post with more than 5 votes. For Stop to make GUI with Java .... Use Qt 5 !!

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