...
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 a comma-separated file (
.csv
) with at least 3 columns, and a header row as shown below . : (More information here)
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 |
|
| 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 |
...
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
.csv
file) (More information here) :
sample | single_end | fastq_1 | fastq_2 | strandedness |
Synapse specimenID | 0 (1 if paired-end) | synID | synID | auto |
...