User: jkbonfield

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jkbonfield70
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Posts by jkbonfield

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Recovering bam files after unknow deletion in the storage
... Firstly, don't mount those drives read-write any more. Read-only from now on or you'll exacerbate any data recovery chance by either yourself or professionals. BAM has specific signatures that data recovery tools are unlikely to spot, but you could, *perhaps* extract them yourself from raw disk im ...
written 2 days ago by jkbonfield70
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Answer: A: How to add RG tag into the optional field in a BAM file
... There is samtools addreplacerg which adds or replaces RG tags in records too, but it is a fixed string rather than derived per barcode. This may be useful if you already have files split up per barcode, but not otherwise. If they're all mixed together, then you'll need to read in a table and do a ...
written 12 months ago by jkbonfield70
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Answer: A: what should a SAM/BAM record contain when there are no quality scores
... In *SAM* format the field is '\*'. In *BAM* format this is replaced by a run of 0xff values to match the same length as the sequence. (I've no idea why.) Note this raises a curious ambiguity. How does a single base read with confidence 9 ('*') get interpreted? ...
written 22 months ago by jkbonfield70
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Answer: A: Sorting samtools output by flag or grepping its tags
... SA:Z: tags appear on the primary reads as well as supplementary ones, therefore the count is higher. Filtering by flags is the best approach. (Hint "samtools flags" give you a handy chart of the numbers.) ...
written 22 months ago by jkbonfield70

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