Hi,
has anyone used syzygy for non-model organisms?
I am trying to use syzygy for my de-novo transcriptome analysis. I have two pooled samples that I have sequenced and have managed to get a full transcriptome which contains some 200k isotigs. Each sample is a pool of 30 individuals. I have then realigned my reads for each sample to the created transcriptome using BWA and would like to find SNPs and INDELs.
Syzygy needs a target info file that includes information on chromosome and position. Since I only have random isotig names, Can I trick syzygy using the same chromosome and creating a fake position? Are these fields required and do they need to be unique?
Also, a dbSNP file seems to be required. What is the format of this file? Since this is a non-model organism, how can I prepare a pseudo-file as suggested in the manual?
Thanks ever so much for your help.
Best,
Dave
has anyone used syzygy for non-model organisms?
I am trying to use syzygy for my de-novo transcriptome analysis. I have two pooled samples that I have sequenced and have managed to get a full transcriptome which contains some 200k isotigs. Each sample is a pool of 30 individuals. I have then realigned my reads for each sample to the created transcriptome using BWA and would like to find SNPs and INDELs.
Syzygy needs a target info file that includes information on chromosome and position. Since I only have random isotig names, Can I trick syzygy using the same chromosome and creating a fake position? Are these fields required and do they need to be unique?
Also, a dbSNP file seems to be required. What is the format of this file? Since this is a non-model organism, how can I prepare a pseudo-file as suggested in the manual?
Thanks ever so much for your help.
Best,
Dave