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  • Raw fastq files uploaded to Synapse by researcher in a folder with name format experiment_name_rnaseq_fastq_date . No white space should be present in the filenames (all filenames should have _ for whitespaces.

  • All experiment and sample related annotations need to be added on Synapse before processing can start. This is a required step so that a sample sheet can be generated to trigger the processing workflow

  • The sample sheet should contain the following information in the following format (saved as a .txt file) :

sample

subject

status

sex

file_1

file_2

lane

parentId

bed_file

output_parent_Id

Synapse specimenID

Synapse individualID

1 (Tumor = 1, Normal 0)

XX or XY

syn://synId

syn://synId

Lane information

SynapseID of parent folder

Synapse ID of BED file (if WES sata)

Synapse ID of folder where all processed files will be indexed

  • The files are pulled into NextFlow workflow setup and processed using the following versions of software:

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