Building Reference

[BJWiley233]

When I follow instructions for building reference with Bowtie2 then when calculating the expression I get the error:

No genome information provided, so genome bam file cannot be generated!

But when using the pre-built reference it works fine. I confirmed all the files are there after building reference.

Any ideas?

[EDIT] It may be worth to mention this only occurs when building using the 2nd option: building references from a set of transcripts.

[BJWiley233]

Just read down further. Nevermind 👍

Thus, we turn on the --output-genome-bam option in the fifth line. Note that this option is only available when you build references from a genome.