What exactly does it mean for a read to be 'mapped in a proper pair' (flag 0x2) as opposed just paired reads (0x1)? I have a bam file where, when I use -f 0x2, I get no output. Does this mean the reads weren't aligned or something?
•
written
by
mrk •
1 answer
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the sequencer.
mapped in a proper pair= the two sam records of a pair are mapped on the sam chromosome, at a good distance, mapped on forward and reverse strand (like a PCR, but it's not a PCR)
Thanks. What determines what constitutes a good distance?
I think tools like BWA use the median distance for each chunk of processed data
Log in to answer this question.
-
How to remove reads with no mate? (ERROR:MATE_NOT_FOUND)
written by lacb •
-
SAM flag
written by tea.vuki •
-
Same strand, same QNAME different FLAG?
written by compuTE
-
Strand specific quantification with strand-splitted BAM files
written by compuTE
-
C. elegans WGS large portion of reads flagged as unmapped with Sam flag 133 and 165
written by tyler.j.kennedy •
-
Filtering BAM file to include PE reads that did not map, even though their mate did
written by nute11a •
-
extract one-side unmapped reads from sam
written by liorglic
-
first and second mate reports by samtools 0x40 and 0x60 FLAGs
written by R •
-
A Question About Samtools Flag "87"
written by lwc628
-
What Does The "Proper Pair" Bitwise Flag Mean In A Sam File?
written by Panos
