Hi @Aqleem12 ! This sounds like the perfect use-case for our Fastq Manifest Format ! This format is specifically for sequences that are already demultiplexed, but don't necessarily adhere to the Casava 1.8 naming convention. Since you have paired-end data, you will want to pay close attention to the paired-end portions of that section. There are a few examples of this sprinkled throughout the forum, here are a few to check out:
Hello,
I have an issue with importing my fastq files into the qiime format using the manifest option. .
Error Message
module: loading 'anaconda/3-4.4.0'
Traceback (most recent call last):
File "/users/bbrown3/anaconda/qiime2-2017.8/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/users/bbrown3/anaconda/qiime2-2017.…
Hello. I am also having difficulty with the import of the fastq (not fastq.gz) files using the manifest approach. I am using the manifest approach since the fastq file names are changed when the sequencing facility runs their in-house script. Indeed, the file names do have underscores, which may play into this issue. I checked my manifest file for trailing spaces and correct headers. I am running qiime2 in VB.
My qiime script :
qiime tools import \
--type 'SampleData[PairedEndSequencesW…
Hello,
I am having an issue with importing my fastq data. I am using the 2017.7 form of QIIME 2.
I am using this as a practice run for when I have the full of my data. My files are under a directory still in their .gz format. The command I have been using to import them is
qiime tools import \
--type SampleData[PairedEndSequencesWithQuality]' \
--input-path import_file_fastq.txt \
--output-path paired-end-demux.qza \
--source-format PairedEndFastqManifestPhred33
However I am not sure…
Let us know if you get stuck!
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