...
| Expand |
|---|
| title | Interrogate the SSCS_DCS.py script to determine how to invoke it. Click here for hints before the answer |
|---|
|
You can often get more information about python scripts by typing the name of the script followed by the -h command.
| Code Block |
|---|
| title | The -h command should show you these options as being the key options to use/consider |
|---|
| -f1 FASTQ1, --fastq1 FASTQ1
fastq read1 file to check
-f2 FASTQ2, --fastq2 FASTQ2
fastq read2 file to check
-p PREFIX, --prefix PREFIX
prefix for output files
-s, --SSCS calculate SSCS sequence, off by default. IF DCS
specificed, automatically on
-m MINIMUM_READS, --minimum_reads MINIMUM_READS
minimum number of reads needed to support SSCS reads
--log LOG name of output log file |
| Code Block |
|---|
| language | bash |
|---|
| title | Using that information, see if you can figure out how to put the command together |
|---|
| collapse | true |
|---|
| SSCS_DCS.py -f1 DED110_CATGGC_L006_R1_001.fastq -f2 DED110_CATGGC_L006_R2_001.fastq -p DED110 -s -m 2 --log SSCS_Log |
|
This should take 10 minutes or less to complete is expected to take more than 30 minutes in an idev shell. You may want run it as a submitted job rather than interatively. If you are unsure how to accomplish this please ask. Suggest looking over the alternative library prep presentation Alternative Library Prep Methods.pdfor the duplex sequencing paper itself in the mean time
...