Prepared by the eResearch Office, QUT.
...
A samplesheet.csv file tells the workflow the location of the read 1 (R1), read 2 (R2) and other information about the samples including ‘group’ (i.e., control or infected), replicate number and the orientation of the reads (i.e., forward, reverse, unstranded).
Example samplesheet.csv (previous versions):
| Code Block |
|---|
group,replicate,fastq_1,fastq_2,strandedness control,1,/path/to/fastq/control-1_R1.fastq.gz,/path/to/fastq/control-1_R2.fastq.gz,unstranded control,2,/path/to/fastq/control-2_R1.fastq.gz,/path/to/fastq/control-2_R2.fastq.gz,unstranded control,3,/path/to/fastq/control-3_R1.fastq.gz,/path/to/fastq/control-3_R2.fastq.gz,unstranded infected,1,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-1_R2.fastq.gz,unstranded infected,2,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-2_R2.fastq.gz,unstranded infected,3,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-3_R2.fastq.gz,unstranded |
Nex format for current version 3.3:
| Code Block |
|---|
group,fastq_1,fastq_2,strandedness control_rep1,/path/to/fastq/control-1_R1.fastq.gz,/path/to/fastq/control-1_R2.fastq.gz,unstranded control_rep2,/path/to/fastq/control-2_R1.fastq.gz,/path/to/fastq/control-2_R2.fastq.gz,unstranded control_rep3,/path/to/fastq/control-3_R1.fastq.gz,/path/to/fastq/control-3_R2.fastq.gz,unstranded infected_rep1,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-1_R2.fastq.gz,unstranded infected_rep2,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-2_R2.fastq.gz,unstranded infected_rep3,/path/to/fastq/infected-1_R1.fastq.gz,/path/to/fastq/infected-3_R2.fastq.gz,unstranded |
...
In the folder you have created for this run create launch.pbs using a text editor (i.e., vim, nano)
...