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8.1 years ago
nuzhat.bt
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0
i have 150 sequenced reads of a particular gene and now i am trying to find SNPs in them. i was trying to use novoSNP but i think i could not handle it properly. kindly guide me how to use novoSNP, what is SQLite file? how to create single SQLite file. how to add reference sequence and run. is there any another free software available?
Hi nuzhat.bt, welcome to Biostars. Unfortunately, novoSNP does not have a proper manual or documentation and I cannot execute it myself. First I suggest to check if it is the right tool for the job at all, as it looks it is for calling SNPs in Sanger sequences only. I don't think an SQLite file is needed, only .ab1 files should be required.
I sometimes use novoSNP, on the rare occasion that I have done Sanger sequencing. It's also developed in my department. In my opinion, the software is quite convenient for automatic variant calling and scoring. (But it's also convenient because it interacts with our LIMS.) Probably good alternatives exist, but I haven't looked into that.
So, nuzhat.bt, can you clarify if sanger sequencing was how you obtained the data and that you have ab1 files?
If you just have 150 reads (which I assume means this is traditional sanger sequencing) and if your main aim is to find SNP's then GeneScreen looks like a free solution. There are some other possibilities here.