Hello, I was trying to look at the scores of paired and unpaired alignments of my paired-end reads(FASTQ) on a reference with bwa mem. From …

Hello to all, I'm studying the SAM specifications, in particular the TLEN field (template length). I found an example of paired-end reads in the SAM …

From the flag bit 8, we can get obtain that the next segment in the template is unmapped so consequently, the read is not paired …

In sam and bam files, flag is used to indicate the alignment state of the read, each flag has 11 positions when expressed as binary …

Is there a tool which will edit the flag for all reads in a BAM file? In my case: The GEM aligner sets the "paired" …

I'm very confused with the meaning of flag 69 and 137. From the explain flag tool https://broadinstitute.github.io/picard/explain-flags.html flag 69 (1+4+64) means: read paired read unmapped …

If a read name is found multiple times in a SAM file, the tag (`NH:i`) is set to indicate how many times that read name …

<p>Hi,</p> <p>I have 100 samples (individuals) and 100 (SNPs) genotyped. I call the SNPs either a WildType (WT) or a Rare-variant (RV) across all samples. …

<p>Hi BioStar users,</p> <p>while removing human contamination from paired-end metagenomic Illumina-shotgun data I ran into a strange problem. In a first step I mapped the …

<p>Hi,</p> <p>I'm currently trying to get truly unique aligning paired-end reads in bowtie2, setting <code>-k 1</code> doesn't help in this case as it just reports …