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I ran bwasw and i noticed several reads which are aligning at more than one location nonspecifically. Which flag has to be used in samtools to get unique alignment if I am working with while mouse genome and single read alignments. Thanks.
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Could you post the given records? I would assume you want the "primary" alignment flag.Originally posted by mathew View Post
Also, could you please be more descriptive in your subject name. I would guess that is why you aren't getting any responses besides me! -
I'm pretty sure that bwa won't set the binary flag to indicate that. You can filter your .bam with samtools view for a minimum mapping quality, reads that map equally well to multiple places should have a mapping quality of 0.Comment
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It does, download the latest code, and try "grep "0x100" *.c":Originally posted by swbarnes2 View Post
The last line is key.bntseq.c: m_seqs = m_holes = 8; m_pac = 0x10000;
bwt_gen.c:#define MIN_AVAILABLE_WORD 0x10000
bwtsw2_aux.c: p->flag |= 0x10000;
bwtsw2_aux.c: ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));Comment
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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 -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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