Sequence alignment parameters

Commands in mothur
1

Hi everyone, I have used V3-V4 region for amplicon sequencing to decipher insect gut mcirobiome . I am first time user of data science and learning concepts for microbiome data analysis. Kindly suggest me what would be the set parameters (Start and end) for aligning sequencing with Silva data base. The command for this step mentioned in Miseq-SOP manual is mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=8)

However, Miseq-SOP is based on V4 amplicon sequencing, I have done V3-V4 region amplicon sequencing. What would be the ideal start=?, end=? To execute the above said command?
primers used are
Forward primer (5 -3 direction) GCCTACGGGNGGCWGCAG
Reverse primer: (5 -3 direction): ACTACHVGGGTATCTAATCC
Kindly help me out.

2

Hi there,

I’d encourage you to follow the tutorial we posted for customizing the coordinates to your region of interest.

Thanks,
Pat

3

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.