User: sacha

gravatar for sacha
sacha1.1k
Reputation:
1,140
Status:
Trusted
Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
1 month ago
Joined:
3 years, 1 month ago
Email:
s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 228 results • page 1 of 23 • next >
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increase BWA sensitivity
... Hi, I would like to remove human reads from a metagenomics NGS dataset ( fastq ). Which parameter from **bwa mem** can I change to increase the sensibility ? ( I would like to align more reads ) Penality score ? Gap open ? Clipping penality ? ...
metagenomics bwa hg19 written 7 weeks ago by sacha1.1k • updated 7 weeks ago by h.mon14k
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Comment: C: plot a bedgraph
... Python !! This is awesome ! Thanks ! ...
written 7 weeks ago by sacha1.1k
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Answer: A: plot a bedgraph
... I just discovered the Sushi package which do the job pretty well ! https://bioconductor.org/packages/release/bioc/html/Sushi.html See [plotbedgraph][1] [1]: https://www.rdocumentation.org/packages/Sushi/versions/1.10.0/topics/plotBedgraph ...
written 7 weeks ago by sacha1.1k
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Comment: C: plot a bedgraph
... Thanks pierre. I will try. I forgot to mention that my bed refer to amplicon. ...
written 7 weeks ago by sacha1.1k
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plot a bedgraph
... Hi , I would like to plot a bed file with numeric values ( = bedgraph). My input data are : chr pos start end value ( value between -1 and 1) exemple : chr19 50906809 50907015 0.8173737057494912 chr19 50909381 50909562 0.2639404477044525 chr19 ...
bed bedgraph rna-seq plot written 7 weeks ago by sacha1.1k
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Detect exon deletion/duplication from NGS amplicon
... Hi, I would like to detect exon duplication and deletion from NGS with panel amplicon strategy. For example, I have all exons of APC sequenced with an average depth > 100. ( exon 17 is covered by 34 amplicons ) How can I detect deletion of exon 3,4 or 5 ? is there any tool or method ? My id ...
amplicon ngs cnv written 8 weeks ago by sacha1.1k • updated 8 weeks ago by Eric T.2.1k
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Comment: A: reads y-position in a bam viewer
... It works ! Thanks guys for your help ! I just need some optimization now. QList > rows; seqan::BamAlignmentRecord record; seqan::readRecord(record, bamFileIn); bool newRow = true; for (auto& row : rows) ...
written 9 weeks ago by sacha1.1k
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Comment: C: reads y-position in a bam viewer
... Ok thanks ! I assume I must use this recursive 'add' function in the following way : > for record in readBam(chromosom, start, end): > add(record) ...
written 9 weeks ago by sacha1.1k
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Comment: C: reads y-position in a bam viewer
... See the picture example bellow. I would like to know where to draw the red read. ( bottom or top) ![enter image description here][1] [1]: https://snag.gy/Zxylpt.jpg ...
written 9 weeks ago by sacha1.1k
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Comment: C: reads y-position in a bam viewer
... An application build with C++/Qt and seqan library under GPL license. ...
written 9 weeks ago by sacha1.1k

Latest awards to sacha

Popular Question 7 weeks ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Count repeat sequence
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Somatic allele frequency from TCGA in non-coding DNA
Scholar 7 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Count repeat sequence
Scholar 9 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 3 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 3 months ago, created a question with more than 1,000 views. For Somatic allele frequency from TCGA in non-coding DNA
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Guru 4 months ago, received more than 100 upvotes.
Scholar 4 months ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 4 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 4 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 4 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 10 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Scholar 13 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 13 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 13 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Epic Question 14 months ago, created a question with more than 10,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 16 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Appreciated 17 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files

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