User: sacha

gravatar for sacha
sacha1.6k
Reputation:
1,580
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Trusted
Location:
France
Website:
http://dridk.me/
Twitter:
dridk
Last seen:
1 month ago
Joined:
3 years, 7 months ago
Email:
s****@labsquare.org

doctor in molecular genetics
Rennes Hospital - genomics laboratory

Posts by sacha

<prev • 255 results • page 1 of 26 • next >
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find major transcript from a specific tissue
... Hi, How can I know which transcript is majoritary used for a specific tissue ? For exemple, I would like to known for CDH1 gene, which transcript is majoritary expressed in stomach . Any database ? ...
database rna-seq written 6 weeks ago by sacha1.6k • updated 5 weeks ago by kristoffer.vittingseerup770
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Comment: C: Pipeline for trusight RNA fusion kit
... Ok. But this is the first step of the pipeline. I expect something more to detect fusion gene. Thanks for the link, I will take a look. ...
written 7 weeks ago by sacha1.6k
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Pipeline for trusight RNA fusion kit
... Hi, Do you have any suggestion of pipeline I can use to detect fusion gene for clinical purpose ? I have data from Illumina [trusight RNA kit.][1] [1]: https://emea.illumina.com/products/by-type/clinical-research-products/trusight-rna-pan-cancer.html ...
rna-seq written 7 weeks ago by sacha1.6k • updated 7 weeks ago by Charles Warden5.6k
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Comment: C: Dna Pattern Matching In Python for Analysis
... Is the previous code the expected result? So, if you have a large dataset, you can avoid creation of matrix. This is not efficient, but will work : patterns = [] seq1 = str(next(SeqIO.parse("test.fa", "fasta")).seq) for i in range(len(seq1)): pattern = list() for ...
written 9 weeks ago by sacha1.6k
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Answer: A: Dna Pattern Matching In Python for Analysis
... Something like this ? #### Input fasta file : test.fa >A AAAAAAAAA >B AAAAACAAG >C GAAAACGAA >D AAAAAAAAT #### Python counter from Bio import SeqIO import pandas as pd from collections import Counter df = pd.DataFrame() for r ...
written 9 weeks ago by sacha1.6k
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Comment: C: edit headers of fasta files
... It is a mistake. I fixed it. Sorry ...
written 9 weeks ago by sacha1.6k
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Answer: A: edit headers of fasta files
... I use [seqkit][1] for fasta manipulation Try to select and replace fasta header with seqkit. Use grep and replace command using regular expression and capture. Something like this : seqkit grep -nr -p "WP_\d+\.\d" test.fa|seqkit replace -p ".+(WP_\d+)\.(\d).+" -r '$1[0-9].$2' output : ...
written 9 weeks ago by sacha1.6k
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Comment: A: Google Dataset Search
... Awesome !! ![enter image description here][1] [1]: https://i.imgur.com/7WjqubK.png ...
written 9 weeks ago by sacha1.6k
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Answer: A: how to count variants par sample per chromosome in a vcf file?
... Split your vcf file by sample and count how many times chromosom appear in each file . FILE=yourfile.vcf for sample in `bcftools query -l $FILE` do bcftools view -c1 -H -s $sample -o ${sample}.vcf $FILE cat ${sample}.vcf |cut -f1|uniq -c > ${sample}.count done ...
written 9 weeks ago by sacha1.6k
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Comment: C: Substractive Genomics Analysis
... So, just remove the header ( with awk for instance) and apply my previous command line. cat test.txt |awk 'BEGIN{keep=0}{if ($0 ~ "^>"){keep=1} if (keep == 1) print($0)}'|grep -P -B5 'Identities = \d+/\d+\s\(([7-9]\d|100)%' ...
written 10 weeks ago by sacha1.6k • updated 9 weeks ago by Sej Modha3.8k

Latest awards to sacha

Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Plotting SNP density along a chromosome from VCF files
Appreciated 9 weeks ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Count repeat sequence
Popular Question 9 weeks ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
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 looking for 16S RNA sequence consensus
Scholar 9 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Voter 9 weeks ago, voted more than 100 times.
Appreciated 10 weeks ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Scholar 10 weeks ago, created an answer that has been accepted. For A: bcftools extract data
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Popular Question 10 weeks ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Appreciated 4 months ago, created a post with more than 5 votes. For Big Browser : a new genom browser in development
Popular Question 4 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: awk filed with different separator
Teacher 5 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 looking for 16S RNA sequence consensus
Great Question 6 months ago, created a question with more than 5,000 views. For Stop to make GUI with Java .... Use Qt 5 !!
Popular Question 7 months ago, created a question with more than 1,000 views. For Somatic allele frequency from TCGA in non-coding DNA
Popular Question 7 months ago, created a question with more than 1,000 views. For looking for 16S RNA sequence consensus
Popular Question 7 months ago, created a question with more than 1,000 views. For Big Browser : a new genom browser in development
Popular Question 7 months ago, created a question with more than 1,000 views. For Count repeat sequence
Scholar 7 months ago, created an answer that has been accepted. For A: bcftools extract data

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