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Admin: Pierre Lindenbaum

gravatar for Pierre Lindenbaum
Reputation:
116,430
Status:
Trusted
Location:
France/Nantes/Institut du Thorax - INSERM UMR1087
Website:
http://plindenbaum.blo...
Twitter:
yokofakun
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
8 years, 11 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 • 8,153 results • page 1 of 816 • next >
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Comment: C: Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
... > ases, the Samtools Flag will be set to 0, the read is NOT paired (no mate) , mapped, on forward strand, it's a PRIMARY alignment > and the SA tag will also be set. because this reads has also some supplementary alignemnts. Some parts of the read map elswhere, you should find some reads w ...
written 1 day ago by Pierre Lindenbaum ♦ 116k
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Comment: C: Genomics (DNA) Pipeline - Example
... nextfow pipelines: https://github.com/search?q=bwa+extension%3Anf+HaplotypeCaller (not python) ...
written 3 days ago by Pierre Lindenbaum ♦ 116k
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Answer: A: How to get number of exons for each transcript in biomart
... ucsc (not biomart) $ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select chrom,name,exonCount from wgEncodeGencodeBasicV28;' +-------+-------------------+-----------+ | chrom | name | exonCount | +-------+-------------------+-----------+ ...
written 3 days ago by Pierre Lindenbaum ♦ 116k
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Answer: A: Edit header of multifasta file
... try sed '/^>/s/\-.*//' input.fa "for the lines starting with '>', subsitute 'everything after "-"' with empty string" ...
written 4 days ago by Pierre Lindenbaum ♦ 116k
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Comment: C: samtools " Assertion `iter->curr_off == iter->off[iter->i].v' failed". "
... is your bam sorted ? is your bai file up-to-date ? ...
written 4 days ago by Pierre Lindenbaum ♦ 116k
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Comment: C: extract fasta sequences using gene names
... look at `grep` with options: `-w` `-A` `-f` ...
written 4 days ago by Pierre Lindenbaum ♦ 116k
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Comment: C: Detecting Klinefelter from genomic files
... use some BAM files from 1000 genomes as positive controls. You need the BAIs but you don't need the whole BAMs, just the headers. https://twitter.com/brent_p/status/1007759165874302976 ...
written 4 days ago by Pierre Lindenbaum ♦ 116k
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Answer: A: Detecting Klinefelter from genomic files
... > Klinefelter syndrome (KS) also known as 47,XXY or XXY, is the set of symptoms that result from two or more X chromosomes in males A first idea would be to use the BAI files of your several bams (affected/non-affected) and use [indexcov][1] to quickly get a chart for the sexual chromosomes: ![ ...
written 5 days ago by Pierre Lindenbaum ♦ 116k
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Comment: C: How to count variant occurrences in .vcf
... for a start: bcftools view input.vcf.gz "chrxxx:12345:12345" |cut -f 10- | tr "\t" "\n" | cut -d ':' -f 1 | sort | uniq -c ...
written 5 days ago by Pierre Lindenbaum ♦ 116k
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Comment: C: why GATK makes things more complicated ?
... > . Do you have any workflow how to do the analysis? https://github.com/gatk-workflows/ > then tried to align with GATK did not work https://meta.stackexchange.com/questions/147616 ...
written 6 days ago by Pierre Lindenbaum ♦ 116k

Latest awards to Pierre Lindenbaum

Scholar 1 day ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Scholar 3 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: What To Cover In A Short Talk On Bioinformatics
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: What To Cover In A Short Talk On Bioinformatics
Great Question 7 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Scholar 9 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Scholar 10 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: What To Cover In A Short Talk On Bioinformatics
Scholar 10 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Scholar 10 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: What To Cover In A Short Talk On Bioinformatics
Scholar 11 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: What To Cover In A Short Talk On Bioinformatics
Scholar 11 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: What To Cover In A Short Talk On Bioinformatics
Popular Question 13 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 17 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 17 days ago, created an answer that has been accepted. For A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
Popular Question 19 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 23 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: Local Blast: Querying A Single Sequence Without Input File. Possible ?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Automatic Data Extraction From Timetree
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Automatic Data Extraction From Timetree
Scholar 27 days ago, created an answer that has been accepted. For A: How To Get Gene Regions +3Kb Upstream
Scholar 29 days ago, created an answer that has been accepted. For A: How To Get Gene Regions +3Kb Upstream
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