trnaseq-fasta [artifact]
Table of Contents
A FASTA-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.
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Provided by
There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.
Required or used by
Description
A trnaseq-fasta is a fasta file of sequences from a single tRNA-seq sample of split that is suitable to be used by anvi-trnaseq to create a trnaseq-db.
Like contigs-fasta files, this file is required to have simple deflines. Take a look at your deflines prior to mapping, and remove anything that is not a digit, an ASCII letter, an underscore, or a dash character. The program anvi-script-reformat-fasta can do this automatically for you with the flag --simplify-names.
We recommend using anvi-run-workflow to create this file from paired-end tRNA-seq reads. The trnaseq-workflow uses illumina-utils to merge FASTQ files that may contain a mixture of fully and partially overlapping reads, which both occur using 100 bp (or shorter) reads containing barcodes due to the length of tRNA. Even with 150 bp reads, there may be pre-tRNA covered by partially but not fully overlapping reads. anvi-script-reformat-fasta comes after illumina-utils in the workflow.
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