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Hello,
I am using picard library in java.
is it possible to make query for a specific readname in a bam file?
thanks
Yu
I am using picard library in java.
is it possible to make query for a specific readname in a bam file?
thanks
Yu
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If you just want one or few reads you could do:Originally posted by jay2008 View Post
DarioCode:samtools view myaln.bam | grep '^myreadname'
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I meant what the API in picard can be used.Comment
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Not sure if it is possible in picard. If helpful, consider that you can send the output of picard to stdout using /dev/stdout as output file and then you could pipe it to samtools or grep. If you can be more specific about what you want to achieve you could get more helpful answers...Originally posted by jay2008 View Post
DarioComment
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bam file can be sorted in two ways: coordinate and queryname (sorted by read name). bam.query is based on coordinate. I can not find any APIs for bam file sorted by queryname. I guess there should be search APIs...Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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