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
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
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