insert size via bamtools stats inner or outer ?
Hi guys,
I've a doubt about the meaning of "insert size" from bamtools stats. I've done this: bamtools stats -in $1 -insert input is a bam produced with read1.fastq and read2.fastq (bwa), in each file reads' length is 100 b
and got an insert size of 241 so I supposed it's outer size = R1+R2+insert
**********************************************
Stats for BAM file(s):
**********************************************
Total reads: 820130832 ...
Average insert size (absolute value): 309.402
Median insert size (absolute value): 241
Advance thanks,
Siva
1 answer
Test it:
// if the alignment is downstream of mate then you can get the end position of the read.
if(al.Position > al.MatePosition){
int outter = abs(al.MatePosition - al.GetEndPosition());
int inner = al.InsertSize;
if(outter != inner){
cerr << "insert length is inner" << end;
}
• 0 views
•
link
updated
by
Ram
•
written
by
Zev.Kronenberg
•
written
by
Zev.Kronenberg
Log in to answer this question.
More posts like this
-
cellranger count error:
written by CRISPYCC •
-
Convert hifi_reads.bam to fastq for CellRanger
written by nwerry •
-
Creating fastq subsets from existing files
written by Zack •
-
CellRanger runs into error when running fastq files from SRA
written by firestar
-
SRA-tools fasterq-dump and cellranger issues
written by vishvak2000 •
-
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
written by DNAngel
-
Estimaing insert size from a pair-end library using bbmap
written by Rogerio Ribeiro •
-
inner-distance plot created by inner_distance.py is always right-skewed
written by Ati •
-
genomeCoverageBed out > mapping out
written by Siva •
-
presence of Adaptators whereas read's =100 b ?
written by Siva •
Relevant resource: http://seqanswers.com/forums/showthread.php?t=15511