trimming the paired end reads with cutadapt
Hi,
I have paired end reads then I tried the below syntax to trim the universal adapters and quality trimming by cutadapt but I faced error always.
[izadi@lbox161 bowtie2-2.2.5]$ $CUT/cutadapt -q 35 -m 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o out.1.fastq -p out.2.fastq L6_1.fq L6_2.fq
cutadapt: error: no such option: -A
What is my fault please?
Thank you
2 answers
Cut adapt is having only the following options.
Adapter type Command-line option
3' adapter -a ADAPTER
5' adapter -g ADAPTER
Anchored 3' adapter -a ADAPTER$
Anchored 5' adapter -g ^ADAPTER
5' or 3' (both possible) -b ADAPTER
For more information with examples: http://cutadapt.readthedocs.org/en/stable/guide.html
Links:
- 3' adapter: http://cutadapt.readthedocs.org/en/stable/guide.html#three-prime-adapters
- 5' adapter: http://cutadapt.readthedocs.org/en/stable/guide.html#five-prime-adapters
- Anchored 3' adapter: http://cutadapt.readthedocs.org/en/stable/guide.html#anchored-3adapters
- Anchored 5' adapter: http://cutadapt.readthedocs.org/en/stable/guide.html#anchored-5adapters
- 5' or 3' (both possible): http://cutadapt.readthedocs.org/en/stable/guide.html#anywhere-adapters
-A is in read the docs, unfortunately (http://cutadapt.readthedocs.org/en/stable/guide.html#trimming-paired-end-reads ). I think they just need to fix their documentation.
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What do you think "no such option: -A" means?
But I used the cutadapt manual syntax
for paired end I should use
-A? What is wrong?Maybe try to use the most recent version of cutadapt, the version I have installed (1.4.1) does not have -A argument option!
Either the documentation is wrong or they have a bug there. Or you're using a version that doesn't match the documentation.