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Admin: Pierre Lindenbaum

gravatar for Pierre Lindenbaum
Reputation:
96,390
Status:
Trusted
Location:
France/Nantes/Institut du Thorax - INSERM UMR1087
Website:
http://plindenbaum.blo...
Twitter:
yokofakun
Scholar ID:
Google Scholar Page
Last seen:
1 day, 18 hours ago
Joined:
7 years, 5 months ago
Email:
p**********@yahoo.fr

Bioinformatics , Genetics

http://twitter.com/yokofakun

http://plindenbaum.blogspot.com

https://github.com/lindenb/jvarkit

 

 

Posts by Pierre Lindenbaum

<prev • 6,132 results • page 1 of 614 • next >
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Comment: C: How to download all the protein sequences (FASTA files) that contain a specific
... first download ftp://ftp.ncbi.nlm.nih.gov/ncbi-asn1/protein_fasta/ then filter https://www.google.fr/search?q=filter+fasta+sequence+site%3Abiostars.org ...
written 2 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: Why are restriction enzymes important to gene cloning?
... Hello snsd.yoona07! We believe that this post does not fit the main topic of this site. not related to bioinfirmatics. see also ; try this site named wikipedia: https://en.wikipedia.org/wiki/Restriction_digest For this reason we have closed your question. This allows us to keep the site focused ...
written 3 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: Sorting samtools output by flag or grepping its tags
... 256 would be used for a read mapping a duplicated gene: a read could have a two possible position (primary + not-primary=256 alignement) a first part of the read is mapped on a region while the other part is clipped. There is a second alignment (2048) for this second part, mapping another region of ...
written 4 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: Sorting samtools output by flag or grepping its tags
... second: 256 if for 'secondary alignment' = an alternative alignment for the current read. I think you want 2048 'supplementary alignement' ...
written 4 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: Sorting samtools output by flag or grepping its tags
... first: how do know there is no 'SA:Z' substring in the quality string ? ...
written 4 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: How to extract all the simple repeats from the hg19 reference genome
... mono-repeat (same base) of len > 5 ...
written 10 days ago by Pierre Lindenbaum ♦ 96k
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Answer: A: How to extract all the simple repeats from the hg19 reference genome
... the following C program will find the simple repeats: https://gist.github.com/lindenb/eade421ffda5e0c71055b514a8f86822 compile gcc biostar267241.c example: curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz" | gunzip -c | ./a.out | grep -E '(981861|1116223 ...
written 10 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: API for gene names by location
... Hello akij! Questions similar to yours can already be found at: Retrieve All Genes Contained Within A Specific Chromosomal Region Using R And Biomart To Get All Genes Within A Genomic Region How Find Genes On Specific Positions How to get all genes for a specific list of regions in R ...
written 11 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: Remove sequences with stop codons from FASTA file
... please, don't be lazy and try to understand how this works. ...
written 12 days ago by Pierre Lindenbaum ♦ 96k
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Comment: C: Remove sequences with stop codons from FASTA file
... it convert the lines back to fasta (transform the '(title)(tab)(seq) to (title)(newline)(seq) see [convert back to fasta][1] [1]: https://gist.github.com/lindenb/2c0d4e11fd8a96d4c345#format-back-to-fasta ...
written 12 days ago by Pierre Lindenbaum ♦ 96k

Latest awards to Pierre Lindenbaum

Appreciated 7 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 7 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How To Combine Two Samtools Commands.
Popular Question 8 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 13 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Appreciated 18 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Scholar 20 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Scholar 23 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Scholar 26 days ago, created an answer that has been accepted. For A: how to write scripts to split GO terms as one per line
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Scholar 27 days ago, created an answer that has been accepted. For A: Variant callers reporting different read depth on same alignment
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Great Question 27 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Good Answer 28 days ago, created an answer that was upvoted at least 5 times. For A: Exon Coordinates Of Hg19 Genome Download
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Appreciated 4 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 4 weeks ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
Scholar 4 weeks ago, created an answer that has been accepted. For A: Variant callers reporting different read depth on same alignment
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Low Resolution Sequence Alignment Visualization
Scholar 4 weeks ago, created an answer that has been accepted. For A: get build 37 positions from dbSNP rsIDs
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