Do you know if the file TCA.454reads.fna contains the "raw" reads, everything that it has been sequenced during a run (even short reads, etc)? Can I imput this file to an aligner software instead of the. sff file that I can extract after AVA alignment? Thank you in advance
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It's all of the reads that passed the filters. It contains all of the same reads as the .sff file; the difference is that the .fna file contains only the trimmed sequence information rather than all of the quality, and trim information.
If you want different information than that, you can use the command line tools (sfffile, sffinfo, etc.) to get different information out of the .sff file (untrimmed reads, read subsets, quality information, rescore the reads, and more).
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