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: how to correct this Error while building index from .bam file?
... validate your bam file. what is the output of `samtools view -c file.bam` ? if there is an error, it doesn't come from `index` but from your upstream workflow. ...
written 2 hours ago by Pierre Lindenbaum113k
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Comment: C: Faster way to get sequences from large fasta files?
... If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. ![Upvote|Bookmark|Accept][1] [1]: http://i68.tinypic.com/2m2ykjr.png ...
written 23 hours ago by Pierre Lindenbaum113k
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Answer: A: Faster way to get sequences from large fasta files?
... linearize your fasa file, sort and use joiin. Not tested but it should be something like join -t $'\t' -1 1 -2 1 \ <(cat query.file | paste - - | cut -c 2- | sort -t $'\t' -k1,1) \ <(sort subject.file) |\ tr "\t" "\n" ...
written 1 day ago by Pierre Lindenbaum113k
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Answer: A: How to generate a BAM/SAM file to show a mutation using BWA aligner
... > So am missing something here ? yes. The 'M' operator doesn't mean that there is a **perfect** match. It means that the two sequences are best aligned if the read and the ref are aligned at this position. You want the derived symbols of 'M' which are '=' (match) and 'X' (mismatch) . See the SA ...
written 1 day ago by Pierre Lindenbaum113k
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Comment: C: Python Script to Calculate Total Number of genes in 3 ORF
... it sounds like a great project ! ...
written 1 day ago by Pierre Lindenbaum113k
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Comment: C: speed up bcftools annotate command
... split the analysis per chromosome ...
written 1 day ago by Pierre Lindenbaum113k
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Answer: A: Difference between proper paired reads and mapped and paired reads
... > reads mapped and paired the input of the mapping was a set of two fastq files R1.fq and R2.fq from a paired end experiment > reads properly paired? reads R1 and R2 from the same segment are mapped on the same chromosome, at a good expected distance with the correct directions. see https: ...
written 2 days ago by Pierre Lindenbaum113k
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Comment: C: Can I read chrom, strand, pos, len from bam files without htslib?
... > So I can include the whole htslib-project in my project what does 'include the whole htslib-project in my project ' means ? are you talking about git submodules ? https://git-scm.com/book/en/v2/Git-Tools-Submodules ...
written 2 days ago by Pierre Lindenbaum113k
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Answer: A: Can I read chrom, strand, pos, len from bam files without htslib?
... `-Ihtslib` means there is a directory named `htslib` in your current directory and this directory a bunch of `*.h` files. if this directory is not in the current working directory , search for it (someting like) find / -type -f -name "sam.h" 2> /dev/null (wait if you have a large server ...
written 2 days ago by Pierre Lindenbaum113k
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Answer: A: How do I get the strand of a read when using htslib?
... in sam.h: /*! @abstract the read is mapped to the reverse strand */ #define BAM_FREVERSE 16 usage: (aln->core.flag & BAM_FREVERSE) ...
written 2 days ago by Pierre Lindenbaum113k

Latest awards to Pierre Lindenbaum

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Where Can I Get Annovar 'Refgene' Format?
Scholar 1 day ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 2 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 2 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 3 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 3 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 3 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Where Can I Get Annovar 'Refgene' Format?
Scholar 10 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Great Question 11 days ago, created a question with more than 5,000 views. For Mapping Snps To Pathways
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Where Can I Get Annovar 'Refgene' Format?
Popular Question 16 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 16 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: tool for bam soft clipping reads within bed file regions
Good Answer 22 days ago, created an answer that was upvoted at least 5 times. For A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
Scholar 22 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Good Answer 22 days ago, created an answer that was upvoted at least 5 times. For A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
Appreciated 22 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: tool for bam soft clipping reads within bed file regions
Scholar 24 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: tool for bam soft clipping reads within bed file regions
Appreciated 26 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 29 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Scholar 29 days ago, created an answer that has been accepted. For A: tool for bam soft clipping reads within bed file regions
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: tool for bam soft clipping reads within bed file regions

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