Showing posts with label fastq quality. Show all posts
Showing posts with label fastq quality. Show all posts

Wednesday, January 25, 2012

Fastx toolkit with illumina fastq file using standard Sanger format

Software: fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Input: fastq file from illumina, standard Sanger format (Phred + 33)
Function: fastx_quality_stats
Description: Generate quality statistic report for fastq as output. Using this report as input to draw quality plot for fastq files.
Error message: fastx_quality_stats: Invalid quality score value (char '#' ord 35 quality value -29) on line 4.
Solution: -Q 33
Solution source: http://seqanswers.com/forums/showthread.php?p=49667
Final command: zcat sample.fastq.gz | fastx_quality_stats -N -Q 33 -o quality.txt