User: danny

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danny0
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Posts by danny

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Comment: C: Remove all reads failing in ValidateSamFile
... Hi Pierre, this is great - can you give an example of what is supposed to look like? And can this tool also remove the mate of a read that is failing? Also, with regards to another question, could one use this tool to remove reads where the read ID occurs more than twice? I have some legacy bams ...
written 5 months ago by danny0
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Remove all reads failing in ValidateSamFile
... My bam has a lot of bad reads that cause it to fail the GATK. I would like to remove them. How can I programmatically remove the reads identified by ValidateSamFile as causing errors? ...
gatk bam sam written 5 months ago by danny0 • updated 5 months ago by Pierre Lindenbaum108k
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Edit/append RG-ID in a bam
... For a sample, I want to **edit** the read group of every read and in the header. I would strongly prefer to not have to split the bam and redo everything with AddReplaceReadGroups. My question is: how can I add a tag (say "_T") to every RG ID in a bam, both in the header and in the reads? ...
read-group bam written 5 months ago by danny0
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A consistent set of reference files that will work well with each other for WEX sequencing and RNA-seq etc.
... We have recently started to do a lot of (human) sequencing of all different kinds and one thing that has been particularly confusing is trying to understand all of the different versions of the different reference data sets (e.g. the reference genome, transcriptome, db_snp, COSMIC, etc.) that are ou ...
fasta references rna-seq sequencing written 21 months ago by danny0 • updated 21 months ago by harold.smith.tarheel4.1k

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