Hello,
Several of you have asked for various additional information, including normalization and raw FASTQ data.
We have updated the format of the input.csv file to provide this additional information. Please see the section 'Input files' here:
https://www.synapse.org/#!Synapse:syn15589870/wiki/592699
Brian
Created by Brian White brian.white Perfect. Thank you @andrewelamb for the answer and update. I've added those missing columns to the fast lane input.csv file. @jracle
Good catch on the fast lane input file, we updated that with more columns after getting that set up.
The main queues will work just like the fast lane queue in therms of file paths. ie. if the file your are looking for is listed as ensg.expr.tsv in the input file, you will want to look for that in input/ensg.expr.tsv. Does that help?
Hi @brian.white ,
Thanks for this update. Just two further questions regarding this input file:
* Could you also update the one from the example file and/or fast lane to reflect these changes? E.g. the new input contains a variable "normalization" but it doesn't seem to be present in the one from the fast lane, so we cannot fully validate our code.
* In the description of the input file for the various *....expr.file * it is indicated that they correspond to the path ("/input/...") to the file. But does this path include the "/input/" folder as indicated there or not? At least in the fast lane it doesn't seem to include it, so we need to add this folder by hand, but will it remain like this in the main queues?
Thank you. Best wishes,
Julien