Changes between Version 57 and Version 58 of SOPs/qc_shortReads

Timestamp:

12/18/20 11:05:31 (4 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -244 +244 @@
     }}}
 
+       * To remove Illumina TruSeq adapters (from the [[https://cutadapt.readthedocs.io/en/stable/guide.html|cutadapt user guide]]):
+{{{
+cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC -o trimmed.1.fastq.gz -p trimmed.2.fastq.gz reads.1.fastq.gz reads.2.fastq.gz
+}}}
+
   * '''Method 2''': [[https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/|Trim Galore!]] combines cutadapt, FastQC, and the ability to guess what your adapters, if -a/-a2 options are not provided:
      * Sample command