Dear all,
I have 2x250 paired-end reads for de novo assembly of bacterial genomes.
The reads were processed with cutadapt to remove Illumina adaptors.
In FastQC I see that I should remove some (~10) bases from the beggining of the reads (both reads in the pair) because of base distribution at this region, even though quality is fine. I also wish to cut the end of the reads dues to low quality; ~10 bases on the first read and ~40 on the second one. This is almost constant in all genomes sequenced.
In the end I wish to filter out too short reads.
I went through cutadapt, trimmomatic and a couple of other tools, but I cannot find how I could cut a defined number of bases from both ends from both reads at the same time as to keep reads paired.
Suggestions would be much appreciated. Any other ideas on how to process these reads?
Thanks!
I have 2x250 paired-end reads for de novo assembly of bacterial genomes.
The reads were processed with cutadapt to remove Illumina adaptors.
In FastQC I see that I should remove some (~10) bases from the beggining of the reads (both reads in the pair) because of base distribution at this region, even though quality is fine. I also wish to cut the end of the reads dues to low quality; ~10 bases on the first read and ~40 on the second one. This is almost constant in all genomes sequenced.
In the end I wish to filter out too short reads.
I went through cutadapt, trimmomatic and a couple of other tools, but I cannot find how I could cut a defined number of bases from both ends from both reads at the same time as to keep reads paired.
Suggestions would be much appreciated. Any other ideas on how to process these reads?
Thanks!
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