Question: trimmomaric command for a fasta file?
0
gravatar for Nadin.asal
2.4 years ago by
Nadin.asal0
Nadin.asal0 wrote:

What is the trimmomaric command for a fasta file? plz help me I do not know what to do? This command is for fastq:

java -jar trimmomatic-0.36.jar PE -phred64 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

What is the command for the fasta file?

trimmomatic • 712 views
ADD COMMENTlink modified 2.4 years ago by RamRS30k • written 2.4 years ago by Nadin.asal0
6

With respect, if you post a sparse question without details but with typos all over the place, you really cannot expect any elaborate answers.

ADD REPLYlink written 2.4 years ago by ATpoint38k

Depends on what you want to do : http://www.usadellab.org/cms/?page=trimmomatic

ADD REPLYlink modified 2.4 years ago by WouterDeCoster44k • written 2.4 years ago by Bastien Hervé4.7k

You don't have quality on fasta file. Thus, you can't use Trimmomatic on fasta file because it is quality based

You can take a look at cutadapt to remove adapters on fasta file

ADD REPLYlink written 2.4 years ago by Bastien Hervé4.7k

thanks So should I download the file fastq?

ADD REPLYlink written 2.4 years ago by Nadin.asal0
2

Please read whats @h.mon linked to you. We don't even know what you are try to do.

Where did you get the data ? sequencer from your lab ? Internet (NCBI...) ?

Why do you want to use Trimmomatic ? Remove adapters or cut reads with bad quality ?

No need to use Trimmomatic if your reads have good quality from end to end.

So should I download the file fastq?

The fastq file of what ?

If you have to chose between fasta and fastq format to download reads always chose fastq format. Fasta is only used for reference annotation

With respect, if you don't know the difference between fasta and fastq you will have to read some documentation to go further. Using tools without knowing what they are doing, what are their input and output is a very bad idea.

So, please be clearer on your topic :)

ADD REPLYlink written 2.4 years ago by Bastien Hervé4.7k

Please provide more information on which data you have and what you aim to achieve. As such we can help you with your question :-)

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k

Hi Nadin.asal,

There is no good reason to delete a post, especially after people have tried to help you.

Cheers,
Wouter

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k

Nadin.asal,

As you insisted on deleting your post repeatedly even after being requested not to, your account has been temporarily suspended. It will be reactivated in 24 hours. Thank you!

--
Ram

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by RamRS30k

I have cleaned this thread of comments which do not help to get to a solution for the OP. I do understand people didn't mean to be offensive, but please keep in mind that what you write might still come across as offensive, especially when users are not native English speakers.

As always, be kind.

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k
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