Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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Posts by Pierre Lindenbaum

<prev • 8,021 results • page 1 of 803 • next >
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Comment: C: Omics Data Analysis: What keeps you up at night
... Hello p.hadjipanayiotou! Questions similar to yours can already be found at: Survey - Tell me about your Bioinformatics struggles We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. ...
written 5 hours ago by Pierre Lindenbaum115k
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Comment: C: Omics Data Analysis: What keeps you up at night
... answering questions about omics data analysis. ...
written 5 hours ago by Pierre Lindenbaum115k
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Comment: C: Biostar Bioinformatics textbooks
... Hello Charles Olweny ! We believe that this post does not fit the main topic of this site. post should be written in the biostars handbook thread For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagre ...
written 7 hours ago by Pierre Lindenbaum115k
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Comment: C: Filtering paired reads when forward is all scRNA-seq barcode sequence
... > but it's a little tricky considering I can't align the forward reads. so R1 won't be mapped but R2 will. And then filter with samtools ...
written 18 hours ago by Pierre Lindenbaum115k
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Comment: C: Generate all bifurkating newick trees given for N taxa
... see https://www.biostars.org/p/276858/ ...
written 19 hours ago by Pierre Lindenbaum115k
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Answer: A: Consensus VCF file from several variant callers
... GATK SelectVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php with ``` --concordance Freebayes.vcf ``` > A site is considered concordant if (1) we are not looking for specific samples and the ...
written 22 hours ago by Pierre Lindenbaum115k
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Comment: C: R package openxlsx and gradient
... how is it related to bioinformatics ? ...
written 1 day ago by Pierre Lindenbaum115k
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Answer: A: Common SNPs among all populations
... using **vcffilterjdk** http://lindenb.github.io/jvarkit/VcfFilterJdk.html an example with 3 populations select.code: final String POP1[]={"S1"}; final String POP2[]={"S2","S3"}; final String POP3[]={"S4","S5"}; final String ALL_POPS[][]={POP1,POP2,POP3}; for(String p ...
written 1 day ago by Pierre Lindenbaum115k
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Answer: A: Dealing with a large sample for variant calling
... > This however, seems very time intensive and computationally cumbersome. What would be the alternatives to this ? GATK hapcaller in **gvcf** mode: https://software.broadinstitute.org/gatk/documentation/article.php?id=3893 ![enter image description here][1] [1]: https://us.v-cdn.net/501979 ...
written 2 days ago by Pierre Lindenbaum115k
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Comment: C: bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
... > As for your second point, I am not really sure what you suggest. Do you mean I should provide one chromosome at a time and run the job in parallel? yes ...
written 2 days ago by Pierre Lindenbaum115k

Latest awards to Pierre Lindenbaum

Appreciated 3 hours ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Commentator 5 hours ago, created a comment with at least 3 up-votes. For C: Recommendation For Cnv Calling Program Based On Depth Of Coverage From Bam
Popular Question 1 day ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 3 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 5 days ago, created an answer that has been accepted. For A: Finding out which genes are covered the most
Great Question 6 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Scholar 7 days ago, created an answer that has been accepted. For A: Finding out which genes are covered the most
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 7 days ago, created an answer that has been accepted. For A: Finding out which genes are covered the most
Appreciated 7 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Popular Question 12 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 14 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 16 days ago, created an answer that has been accepted. For A: Finding out which genes are covered the most
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 17 days ago, created an answer that has been accepted. For A: Finding out which genes are covered the most
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 21 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 21 days ago, created an answer that has been accepted. For A: Finding out which genes are covered the most
Great Question 21 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Appreciated 21 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 23 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions

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