How to count BAM reads

1

I’ve been using IGV to visualize my BAM files, but I need to calculate the FPKM values by hand. Counting the number of reads by hand is almost impossible and tedious to do. Is it possible to quantify reads in a BAM file?

2

Welcome @dwarner

Would a tool like this one help?

  • FPKM Count calculates raw read count, FPM, and FPKM for each gene (link at EU server → Galaxy)

If you just want straight coverage, for example to create a bigWig file, there are many options. Let us know and we can make more suggestions. Thanks! :slight_smile: