Generatin expression level file from Bam file
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9.7 years ago
machalita • 0

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!

RNA-Seq • 1.4k views
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9.7 years ago
Manvendra Singh ★ 2.2k
ht-seq count is your friend or bamcov from bed tools
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Or featureCounts, which is faster than htseq-count.

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