RNA-seq: How to get an information about breakpoint position of junction reads
Hi I have a RNA-seq data BAM file. I want to check the Defective viral genome, and I can check the read junction in IGV. But I need a file that record the Reads' breakpoint.
EX: Readname | breakpoint position(5') | breakpoint position(3')
I used to the bedtool bamtobed but it just record the reads position in column 2 & 3
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Where can I get gtf file for Adenovirus 5?
written by new •
-
Distinguishing between ambiguously mapped reads in a split bamToBed file
written by rubic
-
How to visualize a pair reads mapped genome.
written by K.Gee •
-
Couting number of similar reads in sam file and output in bed file?
written by bobbyle0210 •
-
Get read start site using bedtools from bam file after merging paired end data
written by snishtala03 •
-
Confirming Viruses detected from NGS data
written by Ron
-
PICARD MarkDuplicates with random barcodes
written by Nicolas Rosewick
-
Generate paired-end fusion read with specific origin and a random destination
written by Nicolas Rosewick
-
How to extract reads supporting protein-coding gene splice junctions from STAR's SJ.out.tab output
written by Nicolas Rosewick
-
Counting reads supporting a specific splice junction from bam file
written by Nicolas Rosewick
