I'm quite new to bioinformatics and apologize for what must be a very basic question – I'd be so grateful for any help!
I'm working on an assembling project using Ion Torrent reads for a genome around 50K bp in length using GS De Novo Assembler and Consed. To assemble in one contig we reduced the number of reads to 30K, but to have more coverage to find weak areas wanted to add back all of the reads. I was able to export the consensus sequence and convert it to an ace file using fasta2Ace.perl and can open this in consed but can't figure out how to add the reads from the original .sff file back in (placed them all in a .fof file). I was trying to make the single consensus sequence a reference sequence but am running into errors for everything I try, I'm not sure if it is because of the Ion Torrent reads - all of the documentation I'm using has info only for 454 and sanger and solexa reads. One of the more common errors I'm getting is that the original .sff file does not exist or cannot be opened, though I can easily get it to open in consed with all of the reads, just not the consenus sequence.
Is there a standard way to compare all reads against a single consensus sequence?
Thanks!
I'm working on an assembling project using Ion Torrent reads for a genome around 50K bp in length using GS De Novo Assembler and Consed. To assemble in one contig we reduced the number of reads to 30K, but to have more coverage to find weak areas wanted to add back all of the reads. I was able to export the consensus sequence and convert it to an ace file using fasta2Ace.perl and can open this in consed but can't figure out how to add the reads from the original .sff file back in (placed them all in a .fof file). I was trying to make the single consensus sequence a reference sequence but am running into errors for everything I try, I'm not sure if it is because of the Ion Torrent reads - all of the documentation I'm using has info only for 454 and sanger and solexa reads. One of the more common errors I'm getting is that the original .sff file does not exist or cannot be opened, though I can easily get it to open in consed with all of the reads, just not the consenus sequence.
Is there a standard way to compare all reads against a single consensus sequence?
Thanks!