Changes between Version 64 and Version 65 of SOPs/qc_shortReads

Timestamp:

10/04/24 14:05:41 (4 months ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -293 +293 @@
    * sample command: 
 {{{
-sbatch -p 20 "fastx_trimmer -f 1 -l 22  -i s7_sequence_clipped.txt -o s7_sequence_clipped_trimmed.txt"  # fastq input and output
-sbatch -p 20 "gunzip -c s7_sequence_clipped.txt | fastx_trimmer -f 1 -l 22 -z -o s7_sequence_clipped_trimmed.txt.gz"  # fastq.gz input and output
+sbatch --partition=20 --job-name=trim --mem=16G --wrap "fastx_trimmer -f 1 -l 22  -i s7_sequences.fastq -o s7_sequences_trimmed.fastq"  # fastq input and output
+sbatch --partition=20 --job-name=trim --mem=16G --wrap "gunzip -c s7_sequences.fastq.gz | fastx_trimmer -f 1 -l 22 -z -o s7_sequences_trimmed.fastq.gz"  # fastq.gz input and output
       
 [-i INFILE]  = FASTA/Q input file. default is STDIN.