User: sacha

gravatar for sacha
sacha710
Reputation:
710
Status:
Trusted
Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
4 hours ago
Joined:
2 years ago
Email:
s****@labsquare.org

Posts by sacha

<prev • 159 results • page 1 of 16 • next >
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Comment: C: REST API to run pipeline ( not Galaxy)
... Thanks, but i would like to know if alternative softwares exists and compare them. I m not sure galaxy provide websocket features. Similar tools should exist outside bioinformatics world. ...
written 5 hours ago by sacha710
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REST API to run pipeline ( not Galaxy)
... I wonder if a framework exists to launch a pipeline / script from a user interface. I mean , something more general than galaxy. I imagine a server with REST endpoint to launch a pipeline and some websockets to monitor your run on live. The UI could be generate from Json-form specification. So, if ...
galaxy pipeline interface launcher written 7 hours ago by sacha710
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Answer: A: Get coordinate of several primer fasta sequence
... So I did it with bowtie2 . And it works perfectly . But I need to generate an index. Blat doesn't need it. [https://github.com/dridk/primersnp][1] [1]: https://github.com/dridk/primersnp ...
written 7 hours ago by sacha710
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Comment: C: Get coordinate of several primer fasta sequence
... That's exactly what I noticed Do you know which parameters are used in BLAT web interface ? Because web interface returns me all alignement. default parameters of blat from console interface don't. ...
written 7 hours ago by sacha710
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Comment: C: Get coordinate of several primer fasta sequence
... Just ran : blat hg19.fa amorce_forward.fa forward.psl let's see what is returning ...
written 11 hours ago by sacha710
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Get coordinate of several primer fasta sequence
... I have several primers in a fasta file (20nt). What's the best way to get genom coordinate of those primers ? Align with bwa ? Other tools ? ...
fasta bed primers alignment coordinate written 12 hours ago by sacha710
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Answer: A: Extract SNPs within 5 bps distance apart
... I guess you can do it with bedtools cluster in two step. http://bedtools.readthedocs.io/en/latest/content/tools/cluster.html?highlight=cluster ...
written 10 days ago by sacha710
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Illumina fastq lane output
... When I convert bcl to fastq (with bcl2fastq), by default I get several fastq file by sample AND by lane. For instance : **PAN150427**_S17_**L001**_R1_001.fastq **PAN150427**_S17_**L002**_R1_001.fastq **PAN150427**_S17_**L003**_R1_001.fastq **PAN150427**_S17_**L004**_R1_001 ...
illumina fastq bcl written 21 days ago by sacha710 • updated 21 days ago by igor3.7k
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Answer: A: FastQt : a clone of FastQC in C++/Qt
... FastQt 0.2 has been released ! - New UI - Drag & Drop - Windows Support and binary avaible - Command Line interface - Exporting results as PNG / SVG - AppImage : Download it and run it from every Linux. Compilation is not necessary ![enter image description here][1] ### For Linux : ...
written 4 weeks ago by sacha710
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remove all leaves from greengene tree
... Hi, I downloaded gg_13_5_otus_99_annotated.tree.gz from [http://greengenes.secondgenome.com/downloads/database/13_5][1] which contains a newick tree of 16S RNA taxonomy. I would like to extract a simple phylogeny tree, for example the relation between g__Straphylococcus, g__Streptococcus and g__E ...
greengene tree newick written 6 weeks ago by sacha710

Latest awards to sacha

Epic Question 9 days ago, created a question with more than 10,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 10 weeks ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Appreciated 3 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Appreciated 4 months ago, created a post with more than 5 votes. For A: Plotting SNP density along a chromosome from VCF files
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
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: Plotting SNP density along a chromosome from VCF files
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Scholar 5 months ago, created an answer that has been accepted. For A: bcftools extract data
Great Question 6 months ago, created a question with more than 5,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Centurion 7 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 7 months ago, created an answer that has been accepted. For A: bcftools extract data
Supporter 8 months ago, voted at least 25 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 12 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Appreciated 12 months ago, created a post with more than 5 votes. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 13 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 15 months ago, created a question with more than 1,000 views. For How bcftools isec works ?
Appreciated 16 months ago, created a post with more than 5 votes. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 21 months ago, created an answer that has been accepted. For A: bcftools extract data

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