User: roryC

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roryC0
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Posts by roryC

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Answer: C: Extracting reads from Pacbio Sequel BAM by read name
... Thanks, On further inspection it is due to the lack of a SM tag in the Pacbio BAM header, which Picard is expecting: https://github.com/PacificBiosciences/blasr/issues/212 The work-around for now looks like running picard with "VALIDATION_STRINGENCY=LENIENT" ...
written 16 months ago by roryC0
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Extracting reads from Pacbio Sequel BAM by read name
... Hi, Does anyone know of a good way to filter reads from a Pacbio BAM file (the Sequel data format)? I have identified some contaminant reads which I would like to remove before mapping the BAM file to my draft assembly using pbalign. I want to use Arrow, so I think it is important to keep the origi ...
sequel arrow pbalign pacbio bam written 16 months ago by roryC0
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Samtools stats "inward oriented pairs" - what flags does this correspond to?
... Hi, I'm trying to understand how Samtools stats designates mapped reads as "inward oriented pairs". I have a mate-pair library contaminated with paired end reads, so I would like to extract the PE reads as an independent file. So far I have the following based on flags and insert sizes: FLAG 83, I ...
alignment sequence samtools sam bam written 2.0 years ago by roryC0 • updated 19 months ago by vo20
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Training Augustus parameters for CDS and UTRs - separately or together?
... Hi, I'm currently looking to train Augustus using optimize_augustus.pl, on a set of 1000 genes with UTRs in genbank format. I'm slightly confused by the instructions given here: http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.UTRTraining where the command is: optimize_augustus. ...
genome gene utr augustus written 2.8 years ago by roryC0

Latest awards to roryC

Scholar 16 months ago, created an answer that has been accepted. For C: Extracting reads from Pacbio Sequel BAM by read name

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