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How can I tell if 454 PE sequences in fasta file format have already been separated?

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  • How can I tell if 454 PE sequences in fasta file format have already been separated?

    Hi

    I am new to bioinformatics and have never worked with 454 PE sequences before. I have 454 PE reads in fasta file format. The sequencing was done on the Roche 454 Titanium platform.

    My understanding is that 454 results are stored in .sff files, from which sequence and quality data must be extracted.

    Is it safe to assume, then, that if I have fasta files the forward and reverse ends have been separated already? I only have one file, not two.

    Is it possible for the ends to still be joined in the fasta file? If so, how can I tell if the PE sequences have been separated already?

    Can anyone suggest tools for doing the separation if I need to? I've found pyrocleaner and the NGS QC Toolkit, but I have no experience with either of them.

    thanks!

    E

  • #2
    You can tell if you either have multiple files for the reads, one with the left end and one with the right end, and perhaps a file with unsplittable (shotgun) reads. Or the names of the sequences can tell you, something like /1 and /2, or read1 and read2, or left and right, or whatever the splitting tool uses. You can splitt using sff_extract, or the newbler program from 454/Roche (perform and assembly and set the '-tr' option on).

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    • #3
      Why don't you just ask from whoever gave you the file?
      savetherhino.org

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