Problem statement:
I have to analyze a illumina paired end data for a 5kb genomic region from rice(japonica) and I am interested to detect the variations in a gene in my 5 different transgenic rice lines. I have one sample sequenced from each line . The sequencing was done using the Sbs-SeqCap method .
Questions:
1) What more information do I need from the wet lab side to do the analysis??
2) I want to understand the variation in all the regions(promoter,cds,terminator etc ) in the gene in all different lines. More the information I can capture,better it is. what would be the workflow ?
3) Do I just need to run the variant calling workflow ? I guess I can do more than that with this data.
This is to get an opinion about the various ways I can approach this problem.
Thanks in advance
I have to analyze a illumina paired end data for a 5kb genomic region from rice(japonica) and I am interested to detect the variations in a gene in my 5 different transgenic rice lines. I have one sample sequenced from each line . The sequencing was done using the Sbs-SeqCap method .
Questions:
1) What more information do I need from the wet lab side to do the analysis??
2) I want to understand the variation in all the regions(promoter,cds,terminator etc ) in the gene in all different lines. More the information I can capture,better it is. what would be the workflow ?
3) Do I just need to run the variant calling workflow ? I guess I can do more than that with this data.
This is to get an opinion about the various ways I can approach this problem.
Thanks in advance
