unmatched number of reads after trimming treatment by afterqc

Question

[德水]

The paried-end raw R1 and R2 are processed by afterqc, and unmatched number of reads in R1 and R2 are generated. Thus, an error information in indicated in the next assembly procedure using SPAdes. Is there any standard method for unmatched number of reads in the paired-end data for further analysis.

[lieven.sterck]

Sounds like an issue with afterQC or with the way you applied it on your data (trimming tools should take care to keep read files in sync when trimming/filtering)

Moreover, the authors of that tools suggest to use their more modern implementation: Fastp . A suggestion I can only support.

[德水]

Thank you so much. Fastp works without error.