...
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
.txtfile) :
sample | subject | status | sex | file_1 | file_2 | lane | parentId |
Synapse specimenID | Synapse individualID | 1 (Tumor = 1, Normal 0) | XX or XY | synID | synID | Lane information | Synapse folder information |
...
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
.csvfiles):
sample | single_end | fastq_1 | fastq_2 | strandedness |
sample_id_1 | 0 (1 if paired-end) | synID | synID | reverse or forward |
sample_id_2 |
...