Hi jstjohn,
in the 'reads' folder there are 2 files generated per library.
*.filtered.readpairs.singles.fasta extension is the filtered file during reading of the paired-read files. This file is filtered on paired-sequences containing N's. If one of the two sequences of a pair contains an 'N' character, the paired-read is discarded.
*.foundpairedreads extension contains the paired-reads used for scaffolding. Keep in mind that we only use the edges of the contigs for mapping the reads, therefore less reads can be mapped (though we don't mind, because they are not very useful for scaffolding).
Sorry that this was not clear.
Boetsie
in the 'reads' folder there are 2 files generated per library.
*.filtered.readpairs.singles.fasta extension is the filtered file during reading of the paired-read files. This file is filtered on paired-sequences containing N's. If one of the two sequences of a pair contains an 'N' character, the paired-read is discarded.
*.foundpairedreads extension contains the paired-reads used for scaffolding. Keep in mind that we only use the edges of the contigs for mapping the reads, therefore less reads can be mapped (though we don't mind, because they are not very useful for scaffolding).
Sorry that this was not clear.
Boetsie
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