Hello,
I have sequences in paired end that have both primers in R1 and R2 files.
For exemple, a sequence in the forward ( R1 ) file :
In bold the 2 primers :
GTACACACCGCCCGTCGCTCCTACCGATACCGGGTGATCCGGTGAACCTTTTGGACCGTTTTTCGGAAAAATAAGTAAACCATATCACCTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCAAGACCAAGTCTCTGCTACCGTACGTCTTCTTAATCTCGTATGCCGTCTTCTGCTTGAAAATTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
A sequence In the reverse ( R2 ) file:
TGATCCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCTAGGTGATATGGTTTACTTATTTTTCCGAAAAACGGTCCAAAAGGTTCACCGGATCACCCGGTATCGGTAGGAGCGACGGGCGGTGTGTACTGTAGAACCATGTCGTCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAACGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
I wish to remove the primers to keep the sequence inside so I used cutadapt like that:
qiime cutadapt trim-paired
--i-demultiplexed-sequences demux-paired-end.qza
--p-front-f GTACACACCGCCCGTC
--p-adapter-f GTAGGTGAACCTGCAGAAGGATCA
--p-front-r TGATCCTTCTGCAGGTTCACCTAC
--p-adapter-r GACGGGCGGTGTGTAC
--p-discard-untrimmed
--verbose
--o-trimmed-sequences trimmed_remove_primers.qza
After that I can see my trimming sequences with this command:
qiime tools extract /
--output-path trimmed_remove_primers /
--input-path trimmed_remove_primers.qza
In the forward ( R1) file, unfortunately I have always the forward primer but the reverse primer (and the downstream sequence) has been correctly removed:
GTACACACCGCCCGTCGCTCCTACCGATACCGGGTGATCCGGTGAACCTTTTGGACCGTTTTTCGGAAAAATAAGTAAACCATATCACCTAGAGGAAGGAGAAGTCGTAACAAGGTTTCC
In the reverse ( R2 ) file, the reverse primer has been correctly removed but the forward primer with the downstream sequence is always here:
GTACACACCGCCCGTCGCTCCTACCGATACCGGGTGATCCGGTGAACCTTTTGGACCGTTTTTCGGAAAAATAAGTAAACCATATCACCTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCAAGACCAAGTCTCTGCTACCGTACGTCTTCTTAATCTCGTATGCCGTCTTCTGCTTGAAAATTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
I don’t undersand why only the reverse primer are removed on the forward (R1) and reverse (R2) file?
After that removing primers step I will use dada2, this is correct right?
Thank you for any advice and have a nice day
Jérémy Tournayre
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