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Conversion of Fasta file

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.

sequence genome sequencing
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updated by Ram Ram • written by M.Nadeem Khan • M.Nadeem Khan

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

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written by Antonio R. Franco Antonio R. Franco

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.

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written by Ram Ram

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
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written by Sej Modha Sej Modha

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

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written by M.Nadeem Khan • M.Nadeem Khan

1 answer

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.

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written by Carlo Yague Carlo Yague

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

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written by M.Nadeem Khan • M.Nadeem Khan

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.

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written by Ram Ram

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