Can ''qwindowaverage'' help me ?


I want to do quality filter of my data by getting rid of the low quality score reads. I have sequences from illumina miseq and I did not get any .qual file. In this case can I use trim.seqs(fasta=…, qwindowaverage=35)? If no, is there any alternative ???

If you have the fastq files from Illumina you can split them into fasta and qual files using These can then be put through the trim.seqs().


Thanks for the response. Can you please explain that after which step I should do Do I have to make qual files for all forward and reverse reads SEPERATELY ?

Or do I have to make a file in notepad as we do for make.contigs command (i.e, like stability.file) and then select that file for doing ?

OR do I have to combine names of qual files of forward and reverse sequences of all libraries after doing for all forward and reverse sequences seperately, And then use this file for mothur > trim.seqs(fasta=sahl09.fna, qfile=sahl09.qual, qaverage=25) ?

Doing this Trim.seqs will from completely throw out the sequence (contig) from analyses ?

Looking forward, Richa

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