Fastqc:how to get a quality score for individual read

[newBioinfo]

Hi Everyone,
I have a 77 million reads and I need to know the quality score of each read so that I can filter the data based on the quality score. I used Fastqc and it gives me the graph of quality score of each read. But I need to know in a file how much is the quality score of each read. Is there any way I can get that.
Please help!!!

[swbarnes2]

Hi Everyone,
I have a 77 million reads and I need to know the quality score of each read so that I can filter the data based on the quality score. I used Fastqc and it gives me the graph of quality score of each read. But I need to know in a file how much is the quality score of each read. Is there any way I can get that.
Please help!!!

I'm pretty sure there is no single value for that. Individual bases have quality scores, a read can have a mapping score, which is entirely dependent on the reference you give it, but I don't know of a single quality score for an Illumina read. You could get all the reads with 80% of the bases >Q30, or trim all the 3' bases with <Q5, or somethinig like that.

[mnkyboy]

You can use fastx to filter based on your desired quality score.

[billstevens]

Sorry, very basic, very quick question. I have very good 100bp PE data (Illumina Phred Scores ~33). That usually holds all the way through from base 1 to 100. However, there are some reads that are low quality, and sometimes, at the 3' end of some reads, the quality dips very low, but not often.

Since the quality doesn't dip often at any end, I think trimming is a bad idea, but I still should filter reads based on a certain quality score, right??

[billstevens]

bump? Sorry for the simple question. I wasn't filtering, but I went to a workshop that said you should always filter/trim, and I just wanted to have one more confirmation.

[billstevens]

Also, sorry, does anyone know how to filter more than one file at a time with Fastq?

[fubar]

Also, sorry, does anyone know how to filter more than one file at a time with Fastq?

Yes is the answer to your question as quoted above.
You might have meant to ask how: I usually filter one or more fastq files using the fastx toolkit wrappers in our local Galaxy which fires off jobs to SGE so I can do 'more than one file at a time' - but YMMV as it always does with these things.