Sunday, January 11, 2015

A note about the original RNA-seq data

I have re-analyzed it down the same pipeline I used for the new data. To keep it consistent with the naming system Josh has implemented, I renamed the files as follows:

Original Name Actual Strain New Name
K_XXX_A kw20 kw20_MX_A
K_XXX_B kw20 kw20_MX_B
S_XXX_A toxx toxx_MX_A
S_XXX_B sxyx sxyx_MX_B
U_XXX_A sxyx sxyx_MX_A
U_XXX_B antx antx_MX_A

Note that a few of the samples were mixed up originally (hence the "Actual Strain" column), this naming scheme takes that into account.

Edit: A key for all the samples has been uploaded to the main folder of the drive as a spreadsheet under the name master_sample_key


Rosie Redfield said...

Shall I go ahead and make the complete 'key' file?

Lauri said...

Thanks for this Scott. I can't find the email where Josh discussed the naming system. It all looks pretty straight forward to me, except I'm not clear on the replicate code. I get that A and B refer to to 2 different replicates of the same sample but what are replicates C through H and why replicate X for rpoD?