- Transcriptomic Data Analysis 57
- FastQC will generate a basic text and a HTML output file that contain
all of the results, including basic statistics, quality score per base and per
sequence, sequence content and so on.
Trimming sequences (optional)
Based on the results of quality control analysis, you may want to remove
the low quality segments or reads for downstream analysis. For example, the
figure of per base sequence quality generated by FastQC reveals that the
quality scores of 3′end of reads are very low (Fig. 4), use “Trim sequence”
tool to remove the low quality regions as follows:
- Expand “NGS: QC and manipulation” in the Tools panel and click “Trim
sequence”. - Under “Library to clip”, click “Multiple datasets” and select all fastq files
for trimming. - If you would like to remove the 10 bases from 3′end of a read length of
100 bps. Set “First base to keep” to “1” and “Last base to keep” to “90”. - Click “Execute” to start the job.
Figure 4. Distribution of per base sequence quality generated by FastQC.