Quality trimming fastq 454 data?

[ewilbanks]

Hi everyone,

Does anyone have suggestions for methods and parameters for effective quality trimming / filtering of 454 data? I have .fastq format data (no sff files )and would like to end trim and remove homopolymers. I don't need a complicated pipeline for other steps, as I've already barcode sorted and trimmed out adapter sequence.

I have tried using FASTX toolkit's fastq_quality_filter which doesn't seem to be working properly, since it fails to remove some parts of the sequence below my set threshold. Has anyone else had this problem? Should I only be using this tool on my Illumina data?

Thanks in advance!
Lizzy

[louis7781x]

Hi ,I studied the same data as you.You can use Galaxy's Build base quality distribution whcih can draw base quality distribution.and then you can saw your data's quality.Generally, That beginning of 5'&3' sequence usually are bad quality.

I want to ask you how to trim adapter? I saw FASTX-TOOLKIT can handle it,but the default dummy adapter. Does it apply to 454's data?

[Jenzo]

I tried prinseq-lite (http://sourceforge.net/projects/prinseq/) for quality filtering. It is also able to trim x bases from the end or beginning, perhaps suitable for you!