Question: Considerations for trimming poor quality Illumina MiSeq paired end reads
gravatar for drthippeshhs
13 months ago by
drthippeshhs0 wrote:

I have generated fastq files from Illumina MiSeq for bacterial genome sequencing. My reads are 2 X 300 bp paired end reads. I checked quality of the reads in FastQC and found that Q score goes below 26 for forward reads from base position 200 and Q score goes below 26 from base position 135 in reverse reads. Also k-mer tab gives failure (X mark) in FastQC report. Reads were around 4 millions for forward and reverse sequencing reads. My question what parameters do I need to consider for trimming poor quality reads (both forward and reverse)? Do I need to trim bases to same length in both forward and reverse reads? What are good parameters for improving QC before proceeding to de novo assembly.

Thanks Thippesh

fastq alignment assembly qa • 779 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by drthippeshhs0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see the tutorials here for advice about QA/QC, including analysis specific examples:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
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