bed file question! [extract read numbers from bed file]
0
0
Entering edit mode
20 months ago
shinyjj ▴ 50

Hi all,

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?enter image description here

In the first row of screenshot, blockSizes show the size of 10 exons. How do I know the read cover among these 10 exons?

BED • 617 views
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

Hello,

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?

ADD REPLY

Login before adding your answer.

Traffic: 2398 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