[Jeremy]

Nigel did you get the refgene.txt file to work? Did you have to change it at all?

I have tried using the xenorefgene.txt (best BLAT alignment of known genes from another species) file for the dog (downloaded from http://hgdownload.cse.ucsc.edu/golde...Fam2/database/) and it keeps giving an error that the line format is not recognizable despite being in the exact same format as the human refgene.txt (as far as I can tell). We even used the dos2unix command on the cluster in case the format of line ends was not correct.

Has anyone had issues like this? I have been in contact with the roche people but that has so far not been helpful.

[Soni]

I have a related question.

I am trying to identify SNPs using gsMapper. I have an annotated reference genome and since my genome is not in USCS I've had to convert the format from gb to refGene using some scripts. As far as I can tell my refGene format is correct. But my output in HCDiff is not accurate. The SNP calls are to the incorrect frame (e.g. frame 2 instead of 3).

Has anyone experienced this? Does anyone know how to rectify this?

Cheers.

[adamdeluca]

The SNP calls are to the incorrect frame (e.g. frame 2 instead of 3).

check your start coordinates

http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1

[Soni]

Thanks for your quick reply adamdeluca. But does this mean gsMapper reads base 0 as the 1st base or do I have to add the base anyway (cos I've done the latter).

If I don't then you might have solved my problem.

Cheers.

[adamdeluca]

all UCSC database formats have start coordinates 0-based, and end coordinates 1-based.

look at an entry in the human refGene table and compare to how it displays in the genome browser.