I have a TXT file:
HISEQ1:105:C0A57ACXX:2:1101:10000:105587/1
HISEQ1:105:C0A57ACXX:2:1101:10000:105587/2
HISEQ1:105:C0A57ACXX:2:1101:10000:121322/1
HISEQ1:105:C0A57ACXX:2:1101:10000:121322/2
HISEQ1:105:C0A57ACXX:2:1101:10000:12798/1
HISEQ1:105:C0A57ACXX:2:1101:10000:12798/2
and a fasta file with sequences:
>HISEQ1:105:C0A57ACXX:2:1101:10000:105587/1
GCACCCTCGGGGGAGCAACGAAGAGGTAGACGAAGGCGATCGCAGCCACCTGCGGCAGTATCCCCAGGAGGTCAAGGTCCTCCTCCCCGCTCACCGTCGCC
>HISEQ1:105:C0A57ACXX:2:1101:10000:105587/2
TTGGTGGCAGGCAACAGCTTTGGACGGCCACCGCCTCATGGCGCCTCCTCCCCGCTGCGTCCTCGCCGCGTCCCTCCCTGCTTCAAGC
>HISEQ1:85:D0C0FABXX:5:1101:1385:36009/1
TTTAGTTCCAGGCCGGCTGAAGACTGTCTTTACAAAAGAAAAGTTTAGCCTAGGAAGCCCATTGTTGTAGGTGTTGTAGTTTTATAGATGTACTTTGGAAA
>HISEQ1:85:D0C0FABXX:5:1101:1385:36009/2
CAGCCAAGTTCGCAGTCTCGATAGTATTGTTTTCATACAGCAGTCTTGACAAACCAAAGTCCGCAACTTTTGGTTCCAGATTATCATCTAGCAATATGTTT
>HISEQ1:105:C0A57ACXX:2:1101:10000:105587/2
TTGGTGGCAGGCAACAGCTTTGGACGGCCACCGCCTCATGGCGCCTCCTCCCCGCTGCGTCCTCGCCGCGTCCCTCCCTGCTTCAAGC
I would like to extract the sequences of these ID's only once from the fasta file and get this output:
>HISEQ1:105:C0A57ACXX:2:1101:10000:105587/1
GCACCCTCGGGGGAGCAACGAAGAGGTAGACGAAGGCGATCGCAGCCACCTGCGGCAGTATCCCCAGGAGGTCAAGGTCCTCCTCCCCGCTCACCGTCGCC
>HISEQ1:105:C0A57ACXX:2:1101:10000:105587/2
TTGGTGGCAGGCAACAGCTTTGGACGGCCACCGCCTCATGGCGCCTCCTCCCCGCTGCGTCCTCGCCGCGTCCCTCCCTGCTTCAAGC
but I get also dublicates. I tried these:
seqkit grep -f in.txt in.fa > out.fa
seqtk subseq in.fa in.txt > out.fa
How to modify the command line above to get unique sequences?
Try with
seqkit grep -f in.txt in.fa | seqkit rmdup -n -o out.fa