Understanding bam tracks
Sorry i am having trouble understanding this concept. For example, when I view a bam file after alignment in igv, I see that there are different tracks that form. How are these tracks formed/why do some aligned sequences belong together or are part of the same track?
When I look at a fastq file, as far as I know I don't believe l there is any indicator of that some reads have any specific relationship with one another?
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Tonkatsu •
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what are these tracks ? alignements+coverage ? the coverage track is calculated from the alignment track.
Hi, sorry for the confusion. I was referring to the gray lines in this picture here. I was wondering why some are in line with each other (same row) as seen by the blue arrow and not with others (red). How is this relationship determined?
IGV just pile-up the reads so they are displayed in a compact way. You can change the order and the grouping algorithm : https://software.broadinstitute.org/software/igv/PopupMenus#AlignmentTrack
I see thanks! So there isn't a way to discern some relationship between reads? They are basically just grouped randomly based on the algorithm set by igv?
define "some relationship"
I guess I am referring to whether some reads were originally closer to each other in the fastq file (sequenced closer in time after one another)?
the position in the fastq file is meaningless.
Thank you for the explanation, is it possible to discern any meaning between reads in terms of position?
what is your biological question?
Are you talking about the colors of the reads?