How can I keep the original fastq file names when I do cutadapt?


when I do paired-end cutadapt, how can I keep the original fastq file names for the output fastq?

for example,

if I use
cutadapt -a ADAPTER_FWD -A ADAPTER_REV -o out.1.fastq -p out.2.fastq T01.R001.reads.1.fastq T02.R002.reads.2.fastq

how can I get “T01.R001.reads.1.trimmed.fastq” and “T02.R002.reads.2.trimmed.fastq”?

I mean I have T01. R001, R002; T01.R001, R002 in each folder.

Thanks for helping!


Hi @Tong_Liu1! I am not entirely sure I understand your question, but in order to import your data to use as a QIIME 2 artifact, you will need to rename you forward reads to forward.fastq.gz and your reverse reads to reverse.fastq.gz. Then, you can import that using something like the following:

$ qiime tools import \
  --type MultiplexedPairedEndBarcodeInSequence \
  --input-path PATH_TO_FILES \
  --output-path multiplexed-pe-seqs.qza

After trimming using qiime cutadapt trim-paired, if you wish to export your data you can check out the Exporting tutorial for more information.

If I have misunderstood your question, can you please provide a concrete example to illustrate? Thanks! :t_rex:


Thanks for you suggestion, and sorry for my late reply! I will try again and let you konw if I have more questions :slightly_smiling_face:

Best regards!


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