Open hubert93 opened 7 years ago
I've trimmed nexteraXT adapter for paired-end illumina data, using this command.
skewer -x CTGTCTCTTATACACATCT sample_1.fastq.gz sample_2.fastq.gz
And i realized that the quality of trimmed read1 is revised to better score. For example,
Raw read1) @MISEQ:70:000000000-AWLU0:1:1101:14472:1001 1:N:0:TAGGCATGAAGGAGTA NTGG ... ACCAGACGGTGAGTAACGAAAGCCAGGGGCGCGAACCGGATTAGAAACCCTTGTAGTCCCTGTCTCT +
Trimmed read1) @MISEQ:70:000000000-AWLU0:1:1101:14472:1001 1:N:0:TAGGCATGAAGGAGTA NTGG ... ACCAGACGGTGAGTAACGAAAGCCAGGGGCGCGAACCGGATTAGAAACCCTTGTAGTCC +
I assume that quality of read1 is corrected by being trimmed adapter sequence using paired-end information. I wonder it is true, and whether there is any way to prevent it.
I've trimmed nexteraXT adapter for paired-end illumina data, using this command.
skewer -x CTGTCTCTTATACACATCT sample_1.fastq.gz sample_2.fastq.gz
And i realized that the quality of trimmed read1 is revised to better score. For example,
Raw read1) @MISEQ:70:000000000-AWLU0:1:1101:14472:1001 1:N:0:TAGGCATGAAGGAGTA NTGG ... ACCAGACGGTGAGTAACGAAAGCCAGGGGCGCGAACCGGATTAGAAACCCTTGTAGTCCCTGTCTCT +
8AC ... 3:C=>5ACGGG>GGFF>7=DGB47CCF7CC@>BD))9ED<C=<6@7CF6C#################
Trimmed read1) @MISEQ:70:000000000-AWLU0:1:1101:14472:1001 1:N:0:TAGGCATGAAGGAGTA NTGG ... ACCAGACGGTGAGTAACGAAAGCCAGGGGCGCGAACCGGATTAGAAACCCTTGTAGTCC +
8AC ... GGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGCCCCC
I assume that quality of read1 is corrected by being trimmed adapter sequence using paired-end information. I wonder it is true, and whether there is any way to prevent it.