Entering edit mode
3.1 years ago
Youyy
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0
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?
Thanks
Skip this quality stuff, if fastqc does not throw an error then it is fine. The per-base quality does not give any valuable information unless fastqc indicates that it is low and therefore a problem during sequencing. You should think about your pipeline. bowtie2 is not a splice-aware aligner so unless you work in bacteria this is the wrong tool. Use something like STAR or hisat2, and cufflinks is old and deprecated. Better something like DESeq2 or edgeR depending onw hat your analysis goal is.
I any case, Galaxy-related questions "how do I do xyz in Galaxy" should be asked at https://help.galaxyproject.org/ which is their dedicated support platform.
Thank you so much.
How about using Tophat? I only have one sample so far, so I didn't do downstream analysis.
Tophat is the splice-aware version of bowtie, very old and deprecated. I suggested two tools above.