I have illumina seq reads of one of my bacteria. I did quality control check in kbase usins FastQC and part of the results as indicated on the attached picture
Could any one advice please on what i should do next with such quality?
Anuraj Nayarisseri I am still new in this so any advice of whether i should trim it amd what program to use be so so helpful
Are you doing a de novo assembly or a reference-based one?
In any case, you should try to trim the bases with a quality lower than a ~30 Phred score or to remove the complete sequences that have low general quality. Did you find any adaptors in your data? If so, you may want to get rid of those sequences, also.
Trimmomatic and bbduk (part of BBtools) are reliant programs to perform this.
In general, you need to assure the reliance on the information before getting into the following steps by removing (cutting or filtering out) low-quality data.
Hi, you could use either cutadapt or trimmomatic specifying the quality threshold to Phred+33 and run FastQC and multiQC again to check :)
I would suggest Trimmomatic tool for adapter removal and quality filter of de novo or reference based reads.
Dear Edwin Wanjofu you can cutadapt or Trimmomatic as Nasreen Bano suggest.. and if want commands for the same please let me know..
best wishes.
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