Shifu Chen

Got your ideas. You mean each plot combines results of all samples.

Seems a good idea, although it may take more effort to implement. I will figure out how to realize that.

As I mentioned above, aggregating all results is not easy and need more effort. I think it may take a couple of weeks, considering that I am also busy on...

AfterQC should be much faster with peppy now. Please try v0.9.4

Thanks, will do that.

" Also lines 287 and 288 of the same file are useless." @serge2016 this file doesn't have line 287, 288. Did you mean [preprocesser.py line 287](https://github.com/OpenGene/AfterQC/blob/master/preprocesser.py#L287) ?

You have to install pypy first. See: http://doc.pypy.org/en/latest/install.html BTW, I suggest to use `fastp`, instead of AfterQC. `fastp` is another tool I developed, providing all AfterQC features, but 10x faster....

It provides similar quality, but much higher performance. But since you have done the first part of analysis using AfterQC, I suggest you to continue use AfterQC for this project....

Thanks, good suggestion. Currently it is ``` -u UNQUALIFIED_BASE_LIMIT, --unqualified_base_limit=UNQUALIFIED_BASE_LIMIT if exists more than unqualified_base_limit bases that quality is lower than qualified quality, then this read/pair is bad. Default 0...

Could you please post the first several lines (i.e. 8 lines) of ../fastq1/SRR1294494_1.fastq.gz and ../fastq1/SRR1294494_2.fastq.gz