mothur

I've obtained raw reads after ITS amplicon sequencing

I am new to bioinformatics, I’ve done with ITS Amplicon sequencing, but i am unable to process my samples.can anyone help me in processing the raw reads

Here is my batch for processing fungal reads

https://github.com/krmaas/bioinformatics/blob/master/mothur.fungal.batch

Ok I’ll check this out. thanks a lot