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

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