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torognes / vsearch

Versatile open-source tool for microbiome analysis
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Could I only output the names of query and target sequences when I use "--usearch_global" function? #486

Closed Statistic-Qin closed 1 year ago

Statistic-Qin commented 2 years ago

I use the --usearch_global funtion for mapping query and target sequences. I find I can use the --fastapairs output the mapped sequences, but I can't only output the paired names. I want the output file like the picutre, which is using the -mapout option in usearch. image

frederic-mahe commented 2 years ago

I am not sure to understand your question, but the --userout and --userfields options allow users to define their own output table:

vsearch \
    --usearch_global <(printf ">s1\nAAAAA\n") \
    --db <(printf ">s2\nAAAAT\n") \
    --minseqlength 1 \
    --id 0.75 \
    --quiet \
    --userfields query+target \
    --userout -
s1  s2
Statistic-Qin commented 2 years ago

Thanks！ That options solved my problem.

frederic-mahe commented 2 years ago

@Statistic-Qin if your problem is solved, then please close the issue