I am working on RNA- seq data. I have a fastq file(single end). After running TOPHAT on the fastq file i am interested in junctions.bed file which is produced. Basically i am interested in reads that start at a particular position , spans the junction and ends at different position. I look my sam/bam file in igv browser and load the junctions.bed file in the browwser. When I take my mouse cursor to junctions graph in the igv browser, i can see the junctions coordinates. For example see figure below:
Now If you see in the image we can see that for rpl3 in one case depth is 872 and coordinates are 1030-2032 with flanking width as (40,67), whereas in other case for rpl3 depth is 16 and coordinates are 1030-2058 with flanking width as (20,63).
Now when i look at the junctions.bed file for rpl3 gene i should get these 2 coordinates as above but instead i get these coordinates as below.
rpl3 990 2099 JUNC00001560 872 + 990 2099 255,0,0 2 40,67 0,1042 rpl3 1010 2121 JUNC00001561 16 + 1010 2121 255,0,0 2 20,63 0,1048
So you see start coordinate is 990 and end coordinate is 2099 but igv shows start coordinate to be 1030 and end coordinate 2032 for the depth 872. Similarly for the other case as well.
So how can i get the real coordinates as i see them in IGV
Hope to hear from you soon