Hello guys,
I've just been hit with my first SOLiD data...
Reading the posts here, I already feel better to see that other people are struggling as well
I'm trying to map the reads (75bp) to prokaryotic reference genomes and detect SNPs. Because I couldn't get any color-space aligners to work I've converted to base-space and used Bowtie2 for alignment. I'm getting on average about 10 mismatches per read. Some have as low as 2 mismatches, but others have above 20. Because I was using ECC chemistry I did not think this would turn out so bad...
My question is this: does it even make sense to try and detect SNPs if I have that many mismatches in my reads? Should I rather focus on getting the alignment to work in color-space?
thanks for your help
I've just been hit with my first SOLiD data...
Reading the posts here, I already feel better to see that other people are struggling as well
I'm trying to map the reads (75bp) to prokaryotic reference genomes and detect SNPs. Because I couldn't get any color-space aligners to work I've converted to base-space and used Bowtie2 for alignment. I'm getting on average about 10 mismatches per read. Some have as low as 2 mismatches, but others have above 20. Because I was using ECC chemistry I did not think this would turn out so bad...
My question is this: does it even make sense to try and detect SNPs if I have that many mismatches in my reads? Should I rather focus on getting the alignment to work in color-space?
thanks for your help
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