Hiiii....If anyone can please helo me how to convert fasta files into fastq using ubuntu....i shall be very thank ful....
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written
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rhoney45 •
4 answers
For those who may happen to reach this thread by way of search in future you can convert a fasta file to fastq format using reformat.sh from BBMap suite.
Please remember that the Q-scores created here are fake (example below sets Q-scores to 35 for all bases).
reformat.sh in=test.fa out=fake.fq qfake=35
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written
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Manvendra Singh
very nice script, Thank you so much! It also works on Mac!
please, the qual string length is one base longer than the sequence length. Could you advise how to solve it?
Hi! The script works unless I use warnings; If I use it, then it gives a warning:
Use of uninitialized value $header in string ne at fasta_to_fastq.pl line 13, <FILE> line 1.
In line 13 is:
if($header ne "") {
Thank you in advance
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written
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katerinavram •
See A: Convert from fasta to fastq for an alternative
You'll have to add my $header; somewhere at the top op the script (aka, declare the variable). I would also advise to add use strict; (next to use warnings)
The simplest and fastest is to use seqtk:
seqtk seq -A input.fq > output.fa
you can always filter out the reads with low quality score from fastq file and then convert to fasta
I think I conveyed some other impression from my comment. I meant that the reads which are not of good quality , e.g. reads containing mostly NNNNNNN , can be removed from fastq and then to be converted to fasta.
Is it right?
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written
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Manvendra Singh
Yes, Indeed.
whoops misread that since it is a strange use case
one can make up quality scores - and it is possible that some tools insist on fastq even though they would not make use of the quality information.
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written
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Istvan Albert
No it won't. But you can see my answer in this thread: A: Convert from fasta to fastq
Remember that the Q scores are fake and you set the value.
Please open a separate question for this issue.
I am trying to make a sam file from it
You will need to add a lot more details here.
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