the insert size in rnaseq

[camelbbs]

HI I have paired-end rnaseq data in sam files like this:

DJG84KN1:219:D0R66ACXX:7:1103:17826:20428	147	chr10	158214	255	95M	=	158144	-165	CTCAAAGAGAAAGCTGTAACTGCTGTTATGTGTCACATACCAAGTTGGAATCCATTTGCCACAGTCTAGGTGACCTCAGCTCACACCTGAGTGGA	DDEEEEEEEFFFFFFHHHHHHJJJJJJJJJJJIJJJJIGJJJIHFJJJJJIJJJJJJJJHEJJJJJJJJJJJGJJJJJJJIIHFCHHFFFFFCCB	XA:i:0	MD:Z:95	NM:i:0

can I ask how much is the insert size (or inner distance)?

[pmiguel]

Technically the "-165" should be the insert size. Well, the absolute value of -165. So "165 bp" is the answer. However this is especially problematic for RNA as you may be mapping cDNA reads derived from spliced mRNA back to genomic DNA. So if your read pairs happen to flank an exon junction or two, you would need to subtract the intron lengths to get the right (or approximately right) answer.

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Phillip