Entering edit mode
4 months ago
Jjbox ▴ 40
I know BED file contains information about exons of every read in blockStarts and blockSizes. Block are aligned exons.
From those, is it possible to count splice junction positions and then count how many distinct reads cover that position?
In the first row of screenshot, blockSizes show the size of 10 exons. How do I know the read cover among these 10 exons?
A BED file is a description of intervals (aka features) on the genome, for example: the positions of exons. Read alignments are something else, typically stored in a BAM file. Read alignments, read numbers, and exon descriptions are not typically stored in the same file type - unless you've constructed this file in a particular way for a very particular reason. (1) What exactly does your BED file represent? (2) Where are your read alignments stored?
1) this BED file represents is one of the outputs using a long read software package. Basically, it contains exon numbers and their sizes.
2) Yes, I do have read alignments separately in BAM file. Are you trying to say I can count the read cover of each junction using BAM file and BED file? Are there any package to do so?