Question: trimming the paired end reads with cutadapt
0
gravatar for F
2.8 years ago by
F3.1k
Iran
F3.1k wrote:

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

 

ADD COMMENTlink modified 2.8 years ago by BioRyder160 • written 2.8 years ago by F3.1k
2

What do you think "no such option: -A" means?

ADD REPLYlink written 2.8 years ago by Devon Ryan86k

but i used the cutadapt manual syntax

cutadapt \
            -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
            -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \
            -o trimmed.1.fastq.gz -p trimmed.2.fastq.gz \
            reads.1.fastq.gz reads.2.fastq.gz

for paired end i should use -A ??? what is wrong?

ADD REPLYlink written 2.8 years ago by F3.1k
1

Maybe try to use the most recent version of cutadapt, the version I have installed (1.4.1) does not have -A argument option!

ADD REPLYlink written 2.8 years ago by b.nota5.4k
1

Either the documentation is wrong or they have a bug there. Or you're using a version that doesn't match the documentation.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Devon Ryan86k
3
gravatar for b.nota
2.8 years ago by
b.nota5.4k
Netherlands
b.nota5.4k wrote:

-A

There is no such option!

ADD COMMENTlink written 2.8 years ago by b.nota5.4k
3
gravatar for BioRyder
2.8 years ago by
BioRyder160
India
BioRyder160 wrote:

Cut adapt is having only the following option.

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 example : http://cutadapt.readthedocs.org/en/stable/guide.html 

ADD COMMENTlink written 2.8 years ago by BioRyder160
2

-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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Devon Ryan86k

Hello Ryan,

Yes, you are right. they have to update their documentation. 

ADD REPLYlink written 2.8 years ago by BioRyder160
1
gravatar for F
2.8 years ago by
F3.1k
Iran
F3.1k wrote:

i should change -A to -g then no error anymore

ADD COMMENTlink written 2.8 years ago by F3.1k
1

yes, for 5' adapter you have to use -g option.

ADD REPLYlink written 2.8 years ago by BioRyder160
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