Understanding bam tracks
0
0
Entering edit mode
12 weeks ago
Tonkatsu ▴ 30

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?

RNA sequencing bam • 686 views
ADD COMMENT
1
Entering edit mode

, I see that there are different tracks that form.

what are these tracks ? alignements+coverage ? the coverage track is calculated from the alignment track.

ADD REPLY
0
Entering edit mode

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?

enter image description here

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

define "some relationship"

ADD REPLY
0
Entering edit mode

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)?

ADD REPLY
2
Entering edit mode

I guess I am referring to whether some reads were originally closer to each other in the fastq file

the position in the fastq file is meaningless.

ADD REPLY
0
Entering edit mode

Thank you for the explanation, is it possible to discern any meaning between reads in terms of position?

ADD REPLY
0
Entering edit mode

what is your biological question?

ADD REPLY

Login before adding your answer.

Traffic: 1536 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6