Generatin expression level file from Bam file

Question

[machalita]

Good morning, not long ago, someone sent me an rna-seq expression level file that looks like this:

NC_014925.1 146 147 146 147 4160
NC_014925.1 147 148 147 148 4161
NC_014925.1 148 149 148 149 4164
NC_014925.1 149 150 149 150 4169
NC_014925.1 150 151 150 151 4167
NC_014925.1 151 154 151 154 4164
NC_014925.1 154 155 154 155 4159
NC_014925.1 155 156 155 156 4161
NC_014925.1 156 157 156 157 4160
NC_014925.1 157 158 157 158 4186
NC_014925.1 158 159 158 159 4185

What I'm trying to do is, create my own expression level files out of BAM files, how can I accomplish this?

Thanks for your help!

Answer 1

[Manvendra Singh]

ht-seq count is your friend or bamcov from bed tools

[Devon Ryan]

Or featureCounts, which is faster than htseq-count.