Fungi ITS trimming in QIIME

[Mantella86 (Martyn)]

Hi everyone i will be using QIIME to analyse fungal data using the primers ITS1F AND ITS2 from earthmicrobiome.

Do i need to use Q2 ITSexpress before using DADA2?

Is the code for ITS express the same every time? I.E

qiime itsxpress trim-pair-output-unmerged\
  --i-per-sample-sequences sequences.qza \
  --p-region ITS1 \
  --p-taxa F \
  --o-trimmed trimmed.qza

qiime itsxpress trim-pair-output-unmerged\
  --i-per-sample-sequences sequences.qza \
  --p-region ITS1 \
  --p-taxa F \
  --p-cluster-id 1.0 \
  --p-threads 2 \
  --o-trimmed trimmed_exact.qza

Thanks in advance.

[colinbrislawn (Colin J Brislawn)]

Hello Martyn,

@Mantella86

Do i need to use Q2 ITSexpress before using DADA2?

You don't have to, but it's a good idea. This helps trim your amplicons so they representing a consistent region of the amplified gene, which especially important for variable length regions like ITS 1 and 2.

@Mantella86

Is the code for ITS express the same every time? I.E

Those are two examples how to run ITSexpress with different settings. The second example adds the
--p-cluster-id 1.0 flag to explicitly use 100% for pre-clustering, and the --p-threads 2 flag to use two threads and double the processing speed!

You can read about all the other settings on the GitHub page.