User: ricardoguerreiro2121

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Posts by ricardoguerreiro2121

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Pysam VariantFile.fetch() without specifying contig
... Brilliant! Sometimes you just have to go around the problems, not force your way through. Danke schön! Ricardo ...
written 5 days ago by ricardoguerreiro21210
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Pysam VariantFile.fetch() without specifying contig
... Hello, I'm using the Pysam module of Python and calling the function: VF = VariantFile("input_file") VF.fetch() seems to retrieve all reads in the file, while this retrieves reads from positions 0 to 1000 in one specific contig: VF.fetch(contig="contig_name", start=0, end=100 ...
vcf python pysam written 5 days ago by ricardoguerreiro21210
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Comment: C: Capping coverage in bam file
... Once again simple, merci bien! Keep up the helpfulness, it really makes a difference for starting researchers like me. ...
written 9 weeks ago by ricardoguerreiro21210
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Comment: C: Capping coverage in bam file
... So fast, thanks! It was basic, I was tired. Now I have a more relevant question. Do I have to create a sequence diccionary for this to work? >Ignoring SAM validation error due to lenient parsing: Error parsing text SAM file. RG ID on SAMRecord not found in header: 10x; File tmp.bam; Line 6 Lin ...
written 9 weeks ago by ricardoguerreiro21210
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Comment: C: Capping coverage in bam file
... Hey! You have amazing tools, thank you! But I'm struggling to do this exactly as you say: $ java -jar ~/Programs/jvarkit/dist/sortsamrefname.jar -T bam /input.bam >[SEVERE][Launcher]There was an error in the command line arguments. Please check your parameters : Expected one or zero argument but ...
written 9 weeks ago by ricardoguerreiro21210

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