Admin: Pierre Lindenbaum

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

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Comment: C: Subtracting one BAM [control] from another BAM [sample].
... add one sample must be named "control" to fit with 'snippet.txt' ...
written 53 minutes ago by Pierre Lindenbaum99k
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Comment: C: Subtracting one BAM [control] from another BAM [sample].
... your two bams are missing a **RG** tag with a sample name to tell which 'rea'd is control, which read is 'case'. See picard AddOrReplaceReadGroups or `--rg-id ` in http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml ...
written 53 minutes ago by Pierre Lindenbaum99k
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Comment: C: Is there any read-mapping package that could map only the first half or the seco
... why don't you just cut your fastq before aligning ? ...
written 5 hours ago by Pierre Lindenbaum99k
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Comment: C: Subtracting one BAM [control] from another BAM [sample].
... > I want subtraction such as if in sample read alignment count is 12 n in control it's 2, resultant BAM should contain 10 read for that specific position. and that's what is doing this small code. ...
written 5 hours ago by Pierre Lindenbaum99k
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Comment: C: Extract gene lists using two files
... as stated : bedtools intersect. > Which command line of bedtools will you suggest for the result? what did you try ? ...
written 13 hours ago by Pierre Lindenbaum99k
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Comment: C: Questions going missing?
... what was the question about. As an administrator, I can see the deleted questions. ...
written 16 hours ago by Pierre Lindenbaum99k
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Answer: A: Extract gene lists using two files
... convert file 1 to bed: cut -f 2 file1.tsv | tr ":" "\t" | tr "-" "\t" | sort -t $'\t' -k1,1 -k2,2n > file1.bed convert file2 to bed awk '{printf("%s\t%s\t%s\t%s\n",$1,$4,$5,$0);}' file2.tsv | sort -t $'\t' -k1,1 -k2,2n > file2.bed get the intersection using bedtools http://bedtools ...
written 18 hours ago by Pierre Lindenbaum99k
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Comment: C: Subtracting one BAM [control] from another BAM [sample].
... > what does it do if control reads are higher than the sample/case reads for a position ? nothing is printed ...
written 20 hours ago by Pierre Lindenbaum99k
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Answer: A: Genotype calls for a list of variable sites
... * call with GATK + option `-L vcf_to_bed.bed` (or `-L ref.vcf` should work too ) * use SelectVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php with option `--concordance` ...
written 20 hours ago by Pierre Lindenbaum99k
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Answer: A: Subtracting one BAM [control] from another BAM [sample].
... merge you control and case using picard: java -jar picard.jar MergeSamFiles I=S1.bam I=S2.bam O=merged.bam using samjdk http://lindenb.github.io/jvarkit/SamJdk.html and the following script: private final List buffer= new ArrayList<>(); private int compareRead(final SAMRe ...
written 22 hours ago by Pierre Lindenbaum99k

Latest awards to Pierre Lindenbaum

Appreciated 1 day ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 3 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Annotate A Vcf File
Scholar 3 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 4 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Appreciated 4 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 5 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Annotate A Vcf File
Appreciated 6 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Commentator 6 days ago, created a comment with at least 3 up-votes. For C: Remove gap from files
Scholar 7 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 7 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Tools To Calculate Average Coverage For A Bam File?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
Scholar 12 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 12 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Appreciated 13 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 16 days ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Student 18 days ago, asked a question with at least 3 up-votes. For Exome Aggregation Consortium (ExAC) database ?
Scholar 20 days ago, created an answer that has been accepted. For A: removing decimal from ENSEMBLE gene ID from deseq2 output
Scholar 20 days ago, created an answer that has been accepted. For A: removing decimal from ENSEMBLE gene ID from deseq2 output
Scholar 21 days ago, created an answer that has been accepted. For A: removing decimal from ENSEMBLE gene ID from deseq2 output
Scholar 21 days ago, created an answer that has been accepted. For A: removing decimal from ENSEMBLE gene ID from deseq2 output

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