Question: How to write a program in Perl that read a FASTQ file? after then, there is a method to convert the quality score from ASCII to numeric?
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gravatar for prototommaso
2.6 years ago by
prototommaso0 wrote:

Hi dears, i'm a new student of bioinformatic, this is my first approach on this field, i will be very grateful if someone of you can help me with this question. If you have problem to write the entire exercise i will be grateful if you can write me some tips. King Regards, Tommaso from Italy.

quality score ascii fastq read perl • 1.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by prototommaso0
1

This looks like an assignment question and will likely be closed. We discourage these because while someone will give you a quick answer it will prevent you from learning the basics.

The actual conversion of the scores can be done based on the information you can find in the WikiPedia page for FASTQ format. You should know how to write the rest of the stuff (reading files, parsing lines, checking to see if the line is has quality scores, doing conversion and writing result out).

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax85k

Could you be more descriptive about your question. a example of Input and Output would suffice. As you're saying that it's your beginner, I would recommend you to use bioperl.

ADD REPLYlink written 2.6 years ago by var121.trading0

Buongiorno Tommaso, this should have been a Question, not a Tutorial. I have moved it to a Question.

ADD REPLYlink written 2.6 years ago by Kevin Blighe61k

Thank for the answers, The input is a nucleotide sequence, as output i need a rode FASTQ file [example at the link]

ADD REPLYlink written 2.6 years ago by prototommaso0

You can't get a FASTQ from an input nucleotide sequence. There is no quality information in that input (unless you have data you haven't told us about). You could create a script which would emulate a FASTQ, and give you some dummy quality scores, but why you'd want to do that I don't know (even as a test assignment :/ )

ADD REPLYlink written 2.6 years ago by Joe17k

If this is not an assignment, consider bioperl libraries in parsing files

ADD REPLYlink written 2.6 years ago by cpad011213k
1

If this is not an assignment, consider biopython libraries in parsing files

;-)

Perl might have been an amazing language for bioinformatics, but frankly, I don't think there is a good enough reason to get started with it now.

ADD REPLYlink written 2.6 years ago by WouterDeCoster44k
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