Hello,
We've done some great 454 runs on some of our favorite microbes, de novo assembled each, sorted the contigs to a database and completed the annotation of all of them, however now I'm sorta stuck in getting to the part where we compare them to look for variation, mostly point mutation and/or small insertions/deletions.
I know the Roche GS Mapper can do such analysis, however it refuses to read my annotation files (all in gff3) as it requires goldenpath type 128 files. And I can't seem to find anything else which would give me a nice output of snp's in genes and possible corresponding changes in amino acids. I have the consensus reads in several formats, but the good thing from the Roche mapper is that it will include the sequence depth (from the sff files) at which the region with a snp was established, as to eliminate false positives.
I've browsed these forums, yet I can't find anyone else with this specific problem. Can someone give me some advice on how I can complete my analysis?
Thanks in advance
We've done some great 454 runs on some of our favorite microbes, de novo assembled each, sorted the contigs to a database and completed the annotation of all of them, however now I'm sorta stuck in getting to the part where we compare them to look for variation, mostly point mutation and/or small insertions/deletions.
I know the Roche GS Mapper can do such analysis, however it refuses to read my annotation files (all in gff3) as it requires goldenpath type 128 files. And I can't seem to find anything else which would give me a nice output of snp's in genes and possible corresponding changes in amino acids. I have the consensus reads in several formats, but the good thing from the Roche mapper is that it will include the sequence depth (from the sff files) at which the region with a snp was established, as to eliminate false positives.
I've browsed these forums, yet I can't find anyone else with this specific problem. Can someone give me some advice on how I can complete my analysis?
Thanks in advance
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