Hi,
I have 100bp PE Illumina sequencing data, I used CLC genomic tool and trimmomatic did trimming respectively, but after trimming, fastqc still show warning signals for my trimmed data, especially for data trimmed by CLC. In addition, with original trimmomatic parameters, I got very low percent trimmed data out of raw reads, around 30% for paired and 30% for unpaired.
I understand that fastqc is used to check how normal the sequencing data are, one of the reason why my data is not normally distributed might because mine is RNA. But by comparing CLC and trimmomatic trimmed data, I found trimmomatic trimmed data' per base GC content and per base sequence content are normal as checked by fastqc, while CLC doesn't give good performance on those two criteria.
So can anyone here give me any suggestions and advise?
Dose RNA data really need to be pass all the criteria in fastqc?
Thanks advance!
I have 100bp PE Illumina sequencing data, I used CLC genomic tool and trimmomatic did trimming respectively, but after trimming, fastqc still show warning signals for my trimmed data, especially for data trimmed by CLC. In addition, with original trimmomatic parameters, I got very low percent trimmed data out of raw reads, around 30% for paired and 30% for unpaired.
I understand that fastqc is used to check how normal the sequencing data are, one of the reason why my data is not normally distributed might because mine is RNA. But by comparing CLC and trimmomatic trimmed data, I found trimmomatic trimmed data' per base GC content and per base sequence content are normal as checked by fastqc, while CLC doesn't give good performance on those two criteria.
So can anyone here give me any suggestions and advise?
Dose RNA data really need to be pass all the criteria in fastqc?
Thanks advance!
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