Convertion of FASTA file to FASTQ file

Question

[sabreenaalam12345]

I have a Fasta sequence of an animal which is a completely new sequence. I need to convert if to FASTQ file to understand about the quality of the sequence as well how many reads,contigs and scaffold does it contain.How can I convert my FASTA file into FASTQ file in linux operating system? Please help

[Trivas]

FASTQ -> FASTA is a one way conversion. You're stripping all of the metadata (read: quality scores) during the conversion and you're left with just the nucleotide sequence. You can "make up" quality scores if you need a fastq file for a specific program or software. If you have your original FASTQ files, you can use your current FASTA file as a reference genome and map your original sequencing reads to your reference and use BAM/SAM files that will give you the rest of the information.

[sabreenaalam12345]

Thanks for your reply.

[Ram]

QUAL score is not metadata; it's part of the data. metadata describes the data. Part of the content in the header line of each FASTQ entry could be construed as metadata, but I'd argue FASTQ has no metadata.

[Pierre Lindenbaum]

I need to convert if to FASTQ file to understand about the quality of the sequence as well how many reads,contigs and scaffold does it contain.

can you please explain this sentence ?

[sabreenaalam12345]

I wanted to know how can i find out the number of reads, contigs and scaffold in my newly synthesized chromosome?

Answer 1

[GenoMax]

I need to convert if to FASTQ file to understand about the quality of the sequence as well how many reads,contigs and scaffold does it contain

That is not how this works. Quality values are encoded in fastq format at the time of sequencing. If you have fasta files. there is NO quality information associated with that sequence. One can convert fasta sequence to fastq format using fake Q scores but that is not going to help here.

If you simply need stats (how many, how long etc) then you can use stats.sh from BBMap suite.

[sabreenaalam12345]

Thank you so much for your reply.will stats.sh from BBMap suite help me to understand how many reads,contigs and scaffold is present in my newly sequenced chromosome? what information will i get from stats.sh from BBMap suite?