Question: Conversion of Fasta file
0
gravatar for M.Nadeem Khan
3 months ago by
Pakistan/Islamabad/Quaid-I-Azam University
M.Nadeem Khan0 wrote:

Hello Folks!! Hope all of you are fine, doing well and everything around you is going well. I have a FASTA file of about 1GB that contains 16s sequences of different bacterial strains. I want to submit my data to NCBI where the only FASTQ format is accepted. I want to change the format but i don't know how to do that. so if anyone can help do reply it urgently. Am a beginner of Computational biology

Moderators' Note: OP does have a QUAL file along with the FASTA file.

sequencing tool sequence genome • 215 views
ADD COMMENTlink modified 3 months ago by RamRS18k • written 3 months ago by M.Nadeem Khan0
1

Fastq stands for fasta files that contains Quality values for every single sequenced base

You can create fasta files by extracting the information from fastq files, but you can't do the reverse without having the quality values

ADD REPLYlink written 3 months ago by Antonio R. Franco3.9k

I know this. thanks for trying to help me out.

ADD REPLYlink modified 12 weeks ago • written 3 months ago by M.Nadeem Khan0

Please avoid words such as "dear". They hold different connotations in different cultures, and in scientific forums, can come across as inappropriate or condescending. Instead of "Dear XYZ", try using "Hi XYZ" or "Hello XYZ". You can even omit it altogether.

ADD REPLYlink modified 3 months ago • written 3 months ago by RamRS18k
1

As previous comments and answers have mentioned, it is not possible to convert a FASTA file to a FASTQ file without quality score information, however, you can always append dummy quality scores, but it is not advisable, especially if you are planning to deposit the data in public repositories.

On a separate note, NCBI accepts FASTA files for ribosomal sequences:

https://submit.ncbi.nlm.nih.gov/subs/genbank/

Prokaryotic rRNA submissions must meet the following requirements:

 - All sequences are prokaryotic
 - All sequences in the FASTA file contain sequences from one of the
   following types: 16S ribosomal RNA, 23S ribosomal RNA, or 16S-23S
   ribosomal RNA intergenic spacer region
ADD REPLYlink modified 3 months ago • written 3 months ago by Sej Modha3.7k

Dear Sej Modha.. I want to submit my data to the SRA portal and it accepts only FASTQ. I have scores but cannot add these

ADD REPLYlink written 3 months ago by M.Nadeem Khan0

This answer your question to convert from fasta to fastq. which will assume qual score of 40.

Please try to find the origin of this fasta file.

A: convert FASTA into FASTQ using linux

ADD REPLYlink modified 3 months ago • written 3 months ago by Medhat7.9k
2
gravatar for Carlo Yague
3 months ago by
Carlo Yague4.3k
Belgium
Carlo Yague4.3k wrote:

Fasta files contain only sequences, while fastq files have both sequences and quality scores. If you want to recreate a fastq file, you'll need afile with the quality scores corresponding to your sequences, such as a QUAL file.

ADD COMMENTlink written 3 months ago by Carlo Yague4.3k

Dear Carlo Yague Thanks for your reply. I have the QAUL file too but as I mentioned early, am a beginner to the computational biology. I don't know how to convert. Is there any tool which can do this? I tried online tools but failed. or is there any such sequence which I could use as a model and do changes in my file? I can add the scores manually as i have these scores but how to add i don't know

ADD REPLYlink written 3 months ago by M.Nadeem Khan0

Then you can just use this tool. There is also this related thread. Good luck ! EDIT: If you are not used to command line tools, I saw also this one with a GUI, but I didn't test it.

ADD REPLYlink modified 3 months ago • written 3 months ago by Carlo Yague4.3k

Use this script to convert your fasta+qual files to fastq format.

Second option is scripts here.

ADD REPLYlink written 3 months ago by genomax57k

I have the QUAL file

You should specify this in the question. I've added it for you now. The presence or absence of a QUAL file makes a lot of difference. The prevailing situation in most institutes/sequencers is that separate QUAL files are no longer provided - the minimum is a FASTQ, and usual is a BAM file.

ADD REPLYlink written 3 months ago by RamRS18k
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