ITSxpress sample processing

Hi,

I have imported ITS samples into qiime2 using this command:
qiime tools import
–type SampleData[PairedEndSequencesWithQuality]
–input-format PairedEndFastqManifestPhred33
–input-path manifest.txt
–output-path sequences.qza

Now which one of the below should I use to extract the ITS1 regions, what is use of p-cluster-id 1.0?

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
Yogesh

Hi @Yogesh_Gupta,
You can see the q2-ITSxpress github page for usage details and descriptions of these parameters, or use the help documentation (qiime itsxpress trim-pair-output-unmerged --help) to get the same information.

Good luck!

@Nicholas_Bokulich,

thanks I am not able to understand the --cluster-id * The percent identity for clustering reads, set to 1 for exact dereplication.

what does it mean? if we do not mention the cluster-id, how does my analysis is going to be affected?

thanks
Yogesh

See the open-access original publication. It describes both what the clustering parameter does and how it impacts the results.

Good luck!

1 Like