Hi All,
My data (paired end reads) come from Illumina GA II using RNAseq technology. There are four data files: 5_1, 5_2, 6_1 and 6_2. 5_1 and 5_2 are the pair end reads from Lane 5 on the flowcell. And 6_1 and 6_2 is the pair from Lane 6. The results of each pair(5_1 comparing to 5_2; 6_1 comparing to 6_2) look similar after FASTQC using the raw data.
But after quality trimming and adapter trimming (I use the same adapters in this step), the FASTQC results of 5_1 vs 5_2 look different, especially in the FASTQC modules "Per Base Sequence Content" and "Overrepresented Kmers". 6_1 vs 6_2 have the same problem. Because they are paired end reads and be trimmed by the same way, generally the FASTQC results should also look similar. Could anybody give me some reasonable explanations? Any reply will be greatly appreciated.
My data (paired end reads) come from Illumina GA II using RNAseq technology. There are four data files: 5_1, 5_2, 6_1 and 6_2. 5_1 and 5_2 are the pair end reads from Lane 5 on the flowcell. And 6_1 and 6_2 is the pair from Lane 6. The results of each pair(5_1 comparing to 5_2; 6_1 comparing to 6_2) look similar after FASTQC using the raw data.
But after quality trimming and adapter trimming (I use the same adapters in this step), the FASTQC results of 5_1 vs 5_2 look different, especially in the FASTQC modules "Per Base Sequence Content" and "Overrepresented Kmers". 6_1 vs 6_2 have the same problem. Because they are paired end reads and be trimmed by the same way, generally the FASTQC results should also look similar. Could anybody give me some reasonable explanations? Any reply will be greatly appreciated.
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