User: sacha

gravatar for sacha
sacha740
Reputation:
740
Status:
Trusted
Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
2 days, 3 hours ago
Joined:
2 years, 3 months ago
Email:
s****@labsquare.org

Posts by sacha

<prev • 177 results • page 1 of 18 • next >
0
votes
0
answers
102
views
0
answers
Comment: C: How to plot venn diagram from vcf-compare output ?
... yes... but I m lazzy :D ! ...
written 3 days ago by sacha740
0
votes
0
answers
102
views
0
answers
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 3 days ago by sacha740 • updated 3 days ago by WouterDeCoster19k
0
votes
3
answers
247
views
3
answers
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 5 weeks ago by sacha740
0
votes
3
answers
247
views
3
answers
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 6 weeks ago by sacha740
0
votes
1
answer
220
views
1
answers
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 8 weeks ago by sacha740
0
votes
1
answer
220
views
1
answers
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 8 weeks ago by sacha740
0
votes
1
answer
220
views
1
answers
Comment: C: MiSeq reagent kit version 3 : bad reads qualities
... I merged my paired-end data with Flash . https://ccb.jhu.edu/software/FLASH/ flash sample_F.fastq sample_R.fastq > merged.fastq merged.fastq contains 500pb read length . But only 60% reads are preserved. ...
written 8 weeks ago by sacha740
0
votes
1
answer
220
views
1
answers
Comment: C: MiSeq reagent kit version 3 : bad reads qualities
... But I lost 40% of my reads by merging and cleaning with Q>10 . ...
written 8 weeks ago by sacha740
0
votes
1
answer
220
views
1
answers
Comment: C: MiSeq reagent kit version 3 : bad reads qualities
... The kit was purchased from illumina ! https://www.illumina.com/products/by-type/sequencing-kits/cluster-gen-sequencing-reagents/miseq-reagent-kit-v3.html ...
written 8 weeks ago by sacha740
7
votes
1
answer
220
views
6 follow
1
answer
MiSeq reagent kit version 3 : bad reads qualities
... we did a 16S RNA analysis using MiSeq kit version 3. This kit makes paired-end reads with a size of 300pb. By merging both reads, we can cover 535 pb of region V3-V5. As you can see in the following plot, qualities of reads are really bad after the nucleotid 250. Is it normal ? Perhaps the strat ...
illumina quality miseq phred fastqt written 8 weeks ago by sacha740 • updated 8 weeks ago by h.mon6.6k

Latest awards to sacha

Scholar 8 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 9 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Epic Question 3 months ago, created a question with more than 10,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 5 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Appreciated 6 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Appreciated 7 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Plotting SNP density along a chromosome from VCF files
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Scholar 8 months ago, created an answer that has been accepted. For A: bcftools extract data
Great Question 9 months ago, created a question with more than 5,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Centurion 10 months ago, created 100 posts.
Scholar 10 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 10 months ago, created an answer that has been accepted. For A: bcftools extract data
Supporter 11 months ago, voted at least 25 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 15 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 15 months ago, created a post with more than 5 votes. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 16 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 18 months ago, created a question with more than 1,000 views. For How bcftools isec works ?
Appreciated 19 months ago, created a post with more than 5 votes. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 24 months ago, created an answer that has been accepted. For A: bcftools extract data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 515 users visited in the last hour