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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Originally posted by mathew View PostI 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.
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!
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Originally posted by swbarnes2 View PostI'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.
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));
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