How to obtain bridge length in paired-reads

[Martino]

Hi,

I am programming a tool in Python (Pysam).

Pysam has many functions. 1 of them is reading an aligned read.

Example of code is shown below:
========================

outfile = pysam.Samfile( tmpfilename, "wh", header = header )
a = pysam.AlignedRead()
a.qname = "read_28833_29006_6945"
a.seq="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG"
a.flag = 99
a.rname = 0
a.pos = 32
a.mapq = 20
a.cigar = ( (0,10), (2,1), (0,25) )
a.mrnm = 0
a.mpos=199
a.isize=167
a.qual="<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<"
a.tags = ( ("NM", 1),
("RG", "L1") )
outfile.write(a)
outfile.close()
=======================

Now, I would like to know which of the variables of 'a' of AlignedRead gives information about the bridge lenght between 2 reads of a sequenced paired-end fragment?

Is that isize? Or is that flag? If it is not given here, how can I obtain that bridge length information?

[steph]

isize is the insert size, so it's probably the information you are looking for.

[Rocketknight]

The 'insert' usually refers to the entire fragment being sequenced, minus adapters, so I presume the insert length would include the sequenced ends as well as the gap in the middle. If pysam isn't counting the reads, then the isize is what you want. If pysam is counting the reads in the insert size, then you want isize-(2*read length).

[maubp]

pysam won't be counting anything - it will be exposing the ISIZE aka TLEN field in the SAM/BAM field. How that was calculated depends on the software which created the SAM/BAM file.