Changes between Version 59 and Version 60 of SOPs/qc_shortReads

Timestamp:

12/18/20 15:25:09 (4 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -246 +246 @@
        * 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.fq.gz -p trimmed.2.fq.gz reads.1.fq.gz reads.2.fq.gz
+# Choose your preferred minimum length.  If this is not set, some output reads may have a length of 0, which can cause downstream applications to fail.  
+cutadapt --minimum-length 25 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -o trimmed.1.fq.gz -p trimmed.2.fq.gz reads.1.fq.gz reads.2.fq.gz
 }}}