User: ricardoguerreiro2121
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Posts by ricardoguerreiro2121
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... Brilliant! Sometimes you just have to go around the problems, not force your way through.
Danke schön!
Ricardo ...
written 5 days ago by
ricardoguerreiro2121 • 0
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... 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 ...
written 5 days ago by
ricardoguerreiro2121 • 0
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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
ricardoguerreiro2121 • 0
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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
ricardoguerreiro2121 • 0
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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
ricardoguerreiro2121 • 0
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