Tong_Liu1
(Tong Liu)
January 2, 2018, 5:30pm
1
Hi!
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!
Tong.
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!
Tong_Liu1
(Tong Liu)
January 16, 2018, 3:33pm
5
Hi!
Thanks for you suggestion, and sorry for my late reply! I will try again and let you konw if I have more questions
Best regards!
Tong
1 Like
system
(system)
Closed
February 16, 2018, 9:33pm
6
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