Import pair-end merged into QIIME2

User Support
1

Cordial greeting. I got pair-end merged and clean sequences from the Sequencing center. They look like
BMilk1.fastq
BMilk2.fastq
...
I made a manifest as it is attached

MetadataMilk.csv (5.1 KB)

And I wrote next code in qiime2 (2018.11)

qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path MetadataMilk.csv --output-path paired-end-demuxMilk.qza --input-format PairedEndFastqManifestPhred33

However I got the next error

An unexpected error has occurred:

'utf-8' codec can't decode byte 0xe1 in position 430: invalid continuation byte

See above for debug info.

What am I doing wrong?

Thanks!

1 Like
2

Hi,

‘utf-8’ codec can’t decode byte 0xe1 in position 430: invalid continuation byte

here you have the link to a post with an answer to this problem: Better location information for "utf-8 can't decode codec..." error

Also…
You say you are trying to import Paired End MERGED sequences, so those R1 and R2 are merged into 1 file, so you should try to use a manifest and the tools for Sinlge End sequences, see; when your sequences are paired end, you get 2 files, commonly named fileR1 and file R2 that contains your Forward and your Reverse sequences and that tool lets you import both parts when they are not merged, so you can merge them later.

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