How to extract the mean quality score of RNAseq for a sample?
Hi, I have my RNA-seq illumina paired-end data, I followed the tuxedo pipeline by the following stools, FastQC-Cutadapt- Bowtie2-Cufflinks on Galaxy
For FastQC, I have information about the per base quality score(for each position) and per sequence quality score(left column are the scores, right column are the sequence counts), for both Read 1 and Read 2, But there is no information about the mean quality scores for all the reads and all the base pairs. How to find the information?
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