Entering edit mode
6.6 years ago
Nadin.asal
•
0
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?
With respect, if you post a sparse question without details but with typos all over the place, you really cannot expect any elaborate answers.
Depends on what you want to do : http://www.usadellab.org/cms/?page=trimmomatic
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
thanks So should I download the file fastq?
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.
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 :)
Please provide more information on which data you have and what you aim to achieve. As such we can help you with your question :-)
Hi Nadin.asal,
There is no good reason to delete a post, especially after people have tried to help you.
Cheers,
Wouter
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
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.