PacBio Data, Fastq File, FASTA

Question

[hashim.rana11]

I possess a Pacbio data FASTA file, and my intention is to transform it into the fastq file format. I desire to execute this conversion on a Linux system.

Your positive comments are highly appreciated. Thank you..

Answer 1

[GenoMax]

You can use reformat.sh from BBMap suite like so.

reformat.sh -Xmx4g in=your.fa out=out.fq qfake=30

Keep in mind that every base gets the Q score of 30, which is fake.

[hashim.rana11]

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Answer 2

[Istvan Albert]

Since the FASTQ format needs information that is not present in FASTA you can't quite make a real FASTQ file, but you can make a fake FASTQ file by adding made up qualities.

You could use a tool like seqtk

seqtk seq
       ...
        -F CHAR   fake FASTQ quality []
      ...

for example if test.fa contains:

>sequence
ATGC

then

 seqtk seq test.fa -F I

prints:

@sequence
ATGC
+
IIII

[hashim.rana11]

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