How to get quality scores of the reads in Miseq pipeline

Hi Team,

I have checked the fasta files generated with make. contigs command which generated quality fasta file for each sample and a combined report. The report has the fields as below.

Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns Expected_Errors.

Out of these which one we need to consider to know which reads are good and which are not.

Kindly let me know the quality parameter to retrieve good quality contigs.

Thanking you,

Hi there,

We generally don’t use that table to help with screening sequences. The only things we look at are generated by summary.seqs and these include the number of ambiguous base calls and the minimum or maximum length. I’d strongly encourage following the process outlined in the MiSeq SOP.