I am interested in finding the sites of inserts (transposable elements) in a genome of interest. The genome have been sequenced using paired end sequencing, and thereafter an alignment was performed to an index created with the wildtype genome and the insert sequence.
samtools flagstat alignment.sorted.bam 2415270 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 2188174 + 0 mapped (90.60%:-nan%) 2415270 + 0 paired in sequencing 1207635 + 0 read1 1207635 + 0 read2 2187112 + 0 properly paired (90.55%:-nan%) 2187284 + 0 with itself and mate mapped 890 + 0 singletons (0.04%:-nan%) 158 + 0 with mate mapped to a different chr 12 + 0 with mate mapped to a different chr (mapQ>=5)
How should I go about finding the number and sites of inserts in this genome? I think I should focus on the reads with mates mapped to a different chromosome. Is it possible to filter by SAMFLAGS to obtain these read? If so, what are the SAMFLAGS I should use?
Thanks in advance for your help!