Admin: Pierre Lindenbaum

Reputation:
101,550
Status:
Trusted
Location:
France/Nantes/Institut du Thorax - INSERM UMR1087
Website:
http://plindenbaum.blo...
Twitter:
yokofakun
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
7 years, 9 months ago
Email:
p**********@yahoo.fr

Posts by Pierre Lindenbaum

<prev • 6,769 results • page 1 of 677 • next >
1
vote
2
answers
91
views
2
answers
Answer: A: Finding difference in read depth between two BAM files
... using samtools mpileup and two bam files: samtools mpileup -f ref.fasta in1.bam in2.bam | cut -f 1,2,4,7 1 101766 19 29 1 101767 19 30 1 101768 19 29 1 101769 123 188 1 101770 122 187 1 101771 122 189 1 101772 122 189 output is : chrom/pos/depth-bam1/depth-bam2 ...
written 2 hours ago by Pierre Lindenbaum102k
0
votes
0
answers
25
views
0
answers
Comment: C: ask for the pdf version book of ' Biostatistics: How It Works '
... Hello liddong7! We believe that this post does not fit the main topic of this site. I'm closing this question as it's not related to bioinformatics. 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 disa ...
written 3 hours ago by Pierre Lindenbaum102k
0
votes
0
answers
25
views
0
answers
Comment: C: ask for the pdf version book of ' Biostatistics: How It Works '
... this book is not free and your question is not related to bioinformatics. closing. ...
written 3 hours ago by Pierre Lindenbaum102k
0
votes
0
answers
82
views
0
answers
Comment: C: What desktop GUI software is proper for a plant transcriptome de novo assembly a
... why would you need a " desktop GUI software" ? ...
written 1 day ago by Pierre Lindenbaum102k
2
votes
1
answer
76
views
1
answers
Answer: A: GATK Haplotype Caller error
... the message is clear: > The provided VCF file is malformed at approximately line number 30824751: unparsable vcf record with allele W there is an error in the REF or ALT column of your VCF, it should be an [ATGC] string but you have a 'W' allele. thrown here: https://github.com/samtools/htsjdk ...
written 1 day ago by Pierre Lindenbaum102k
0
votes
1
answer
94
views
1
answers
Answer: A: vcftools keep only indels not working
... The error is raised here: https://github.com/vcftools/vcftools/blob/master/src/cpp/header.cpp#L141 in your VCF header you should have: ##INFO= ...
written 1 day ago by Pierre Lindenbaum102k
1
vote
0
answers
131
views
0
answers
Comment: C: Modify FASTA headers
... example of input is neded. ...
written 2 days ago by Pierre Lindenbaum102k
0
votes
0
answers
84
views
0
answers
Comment: C: PICARD ValidateSamFile terminating prematurely, without errors, processes only p
... java 1..7 has been deprecated: http://www.oracle.com/technetwork/java/javase/downloads/java-se-jre-7-download-432155.html > This release is no longer the most current release of Java SE update java to 1.8... ...
written 3 days ago by Pierre Lindenbaum102k
0
votes
0
answers
84
views
0
answers
Comment: C: PICARD ValidateSamFile terminating prematurely, without errors, processes only p
... your version of picard is outdated. 1.67 there is more than 500 bug fixes/commit since 1.67. Update picard and try again please. https://github.com/broadinstitute/picard/releases/tag/2.16.0 ...
written 3 days ago by Pierre Lindenbaum102k
0
votes
1
answer
93
views
1
answers
Answer: A: Getting a sample of 1000 random SNPs with MAF
... using [vcffilterjdk][1] follow by awk | sort: $ curl "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz" |\ gunzip -c |\ java -jar dist/vcffilterjdk.jar -e 'return variant.getAttributeAsList("AF").stream(). ...
written 4 days ago by Pierre Lindenbaum102k

Latest awards to Pierre Lindenbaum

Popular Question 3 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 4 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 4 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Scholar 4 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 6 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
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 many ID's exist in BioSample?
Appreciated 8 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 14 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Scholar 14 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Popular Question 15 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Scholar 15 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Appreciated 17 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Popular Question 19 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 21 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Popular Question 23 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 23 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1333 users visited in the last hour