User: sacha

gravatar for sacha
sacha730
Reputation:
730
Status:
Trusted
Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
6 days, 2 hours ago
Joined:
2 years, 1 month ago
Email:
s****@labsquare.org

Posts by sacha

<prev • 175 results • page 1 of 18 • next >
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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 7 days ago by sacha730
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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 10 days ago by sacha730
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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 27 days ago by sacha730
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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 27 days ago by sacha730
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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 27 days ago by sacha730
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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 27 days ago by sacha730
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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 27 days ago by sacha730
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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 27 days ago by sacha730 • updated 27 days ago by h.mon5.7k
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Comment: C: generate fastq with bed file
... fasta to fastq is easy ! ...
written 27 days ago by sacha730
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Comment: C: R multiple parameters
... I renamed to clarify. arguments[[NUMBER]] are positionnal arguments : function(a,b,c .. ) arguments[[STRING]] are named arguments : function(color="red") ...
written 4 weeks ago by sacha730

Latest awards to sacha

Scholar 27 days ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 4 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Epic Question 8 weeks ago, created a question with more than 10,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
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Appreciated 5 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Appreciated 6 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Plotting SNP density along a chromosome from VCF files
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Scholar 7 months ago, created an answer that has been accepted. For A: bcftools extract data
Great Question 8 months ago, created a question with more than 5,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Centurion 9 months ago, created 100 posts.
Scholar 9 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 9 months ago, created an answer that has been accepted. For A: bcftools extract data
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Popular Question 11 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
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Scholar 14 months ago, created an answer that has been accepted. For A: bcftools extract data
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