User: sacha

gravatar for sacha
sacha1.3k
Reputation:
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Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
2 weeks, 1 day ago
Joined:
3 years, 3 months ago
Email:
s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 240 results • page 1 of 24 • next >
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Comment: C: CuteVariant : A GUI to filter VCF file
... It should works for all kind of vcf ...
written 15 days ago by sacha1.3k
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Answer: A: CuteVariant : A GUI to filter VCF file
... Alpha release 0.1 avaible for Linux as [AppImage][2]. wget https://github.com/labsquare/CuteVariant/releases/download/untagged-7a62372818b54b6974df/CuteVariant-0.1-x86_64.AppImage chmod +x CuteVariant-0.1-x86_64.AppImage ./CuteVariant-0.1-x86_64.AppImage ![screencast][1] You can ...
written 16 days ago by sacha1.3k
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Answer: A: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... Use everything else but not excel . This software is to difficult to use. For example with Python, this code will answer to your question. 4 lines only... import pandas as pd df = pd.read_excel("test.xlsx","test") for i in df.columns: print(df[i].sort_values(asce ...
written 17 days ago by sacha1.3k
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Answer: A: Finding Kmers From Fasta File
... Use [jellyfish][1] This is your test.fa >test TAATGCCATGGGATGTT You want to count all 3-mers jellyfish count -m 3 -s 100000 test.fa -o test.jf jellyfish dump -c test.jf The last command returns : TGT 1 GAT 1 GGG 1 GGA 1 CAT 1 TGC 1 ...
written 17 days ago by sacha1.3k
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Comment: C: Create a File format to store Variant
... where and How to participate? ...
written 24 days ago by sacha1.3k
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Comment: C: Create a File format to store Variant
... :D I know this xkcd too ! That's why I am asking . I didn't find any standard which store variant in hierarchical structure. VCF or BED file doesn't store hgvs notation. Same for patient Ids or family Ids. So, it is 0 standard to 1 standard actually ! ...
written 25 days ago by sacha1.3k
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8 follow
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Forum: Create a File format to store Variant
... Hi, BED format or VCF format are not well designed to store [hgvs][1] notation and metadatas of a variant. I would like to have a specific file format to store list of variant using hgvs notation with different kind of data and make it easier to share, import, export ... For instance, here is ...
hgvs forum json variant standard written 25 days ago by sacha1.3k • updated 25 days ago by d-cameron1.8k
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Twist Bioscience BAM example
... Hi, Does someone have Fastq or BAM data to share from [Twist Bioscience][1] capture kit? I would like to see how read depth looks like. Thanks [1]: https://twistbioscience.com/company/press/twist-launches-exome-and-target-enrichment-solutions ...
data twist bam capture written 29 days ago by sacha1.3k
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Answer: A: Help finding all allele combinations using Python
... I m not sure I understand well... Could you explain what "0,1,2" mean exactly ? And post a tiny example with input and output with 2 snp only ? An idea would be to create a graphe and find all path from start to end. ![graph example][1] [1]: https://framapic.org/ytimGQLPVy4r/eg4DTAfa0WoB.p ...
written 7 weeks ago by sacha1.3k
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Answer: A: Is there a way to save a specific Gene in IGV of a whole exome sample?
... Something like this ? bedtools intersect -a exome.bam -b mygene.bed > mygene.bam ...
written 7 weeks ago by sacha1.3k

Latest awards to sacha

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Great Question 3 months ago, created a question with more than 5,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Popular Question 3 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 3 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 3 months ago, created a question with more than 1,000 views. For Count repeat sequence
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
Scholar 3 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 3 months ago, created a question with more than 1,000 views. For Count repeat sequence
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 5 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 5 months ago, created a question with more than 1,000 views. For Somatic allele frequency from TCGA in non-coding DNA
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Guru 6 months ago, received more than 100 upvotes.
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: awk filed with different separator
Popular Question 6 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 6 months ago, created a question with more than 1,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Scholar 6 months ago, created an answer that has been accepted. For A: bcftools extract data
Popular Question 12 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Scholar 15 months ago, created an answer that has been accepted. For A: bcftools extract data
Scholar 15 months ago, created an answer that has been accepted. For A: bcftools extract data

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