Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Comment: C: Scatter plot for GSEA results analysis
... This post was cited in: > Programming of Schwann Cells by Lats1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis . Cancer Cell. Volume 33, Issue 2, p292–308.e7, 12 February 2018 https://doi.org/10.1016/j.ccell.2018.01.005 ...
written 17 hours ago by Pierre Lindenbaum104k
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Answer: A: Picard MarkDuplicates /SAM validation error
... use https://broadinstitute.github.io/picard/command-line-overview.html#StandardOptions VALIDATION_STRINGENCY=LENIENT ...
written 1 day ago by Pierre Lindenbaum104k
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Answer: A: How Do You Manage Your Files & Directories For Your Projects ?
... 7.8 years later: > Leon Eyrich Jessin : How to organize a project > >" The most important talk you never heard!" > > Hackinars in Bioinformatics > > February 8th 2018 https://github.com/leonjessen/talks/blob/master/presentations/20180208_hackinar_project_organisation.pdf ...
written 1 day ago by Pierre Lindenbaum104k
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Answer: C: create a track with mismatch density from a SAM/bam file
... NM is not always in the $12 , the END position of a read on the REF is not START+read_len (indels, clipping......) here is a solution using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html java -jar dist/bioalcidaejdk.jar -e 'stream().filter(R->!R.getReadUnmappedFlag() &a ...
written 1 day ago by Pierre Lindenbaum104k
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Comment: C: create a track with mismatch density from a SAM/bam file
... > how I could parse a SAM/BAM and count differences .... relates to "Getting number of mismatches from bam record " where no solution was posted so far what about Zev's solution: the NM tag ? ...
written 1 day ago by Pierre Lindenbaum104k
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Answer: A: How to convert string into fasta using bash?
... echo -e '>GA1redu 691-707f 57.9 product 2894bp 2006\r\nGCAGGACTCGGCTTGCT\r\n>HIVRES2redu \r\nGCTCTTGATAAATTTGATATGTCCAT' | tr -d '\r' ...
written 1 day ago by Pierre Lindenbaum104k
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Comment: C: blast using python
... > I also don't think parsing the .xml output of blast is a good idea why ? ...
written 1 day ago by Pierre Lindenbaum104k
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Answer: A: Parsing Standalone Blast XML Output with Biopython on Linux
... in save_file.write('>%s\n') there is only one palceholder '%s' while there are 4 arguments. https://www.safaribooksonline.com/library/view/python-cookbook-2nd/0596007973/ch04s21.html ...
written 1 day ago by Pierre Lindenbaum104k
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Comment: C: Replacing the Chr names and position notions in vcf
... this code doesn't change the VCF dictionary headers ("## contig=....") ...
written 1 day ago by Pierre Lindenbaum104k
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Answer: A: Replacing the Chr names and position notions in vcf
... use `bcftools annotate` https://samtools.github.io/bcftools/bcftools.html with > --rename-chrs file > rename chromosomes according to the map in file, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line. ...
written 1 day ago by Pierre Lindenbaum104k

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Scholar 5 days ago, created an answer that has been accepted. For A: Bedtools Invalid record, record does not exist
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