I have a need to calculate the following, and wonder if anyone else has done something similar or could advise me on how to do it. The question is:
For each base position on a reference sequence, what is the proportion of mapped reads with an A/G/C/T at this position?
e.g. for reference position x, 50% of reads show an A/50% of reads show a T.
At the moment I have Illumina paired end 51bp data and some 76bp data and have mapped the reads to a reference using the maq software. Any advice oon how to do this type of downstream analysis would be much appreciated, thanks.
Lindsey
For each base position on a reference sequence, what is the proportion of mapped reads with an A/G/C/T at this position?
e.g. for reference position x, 50% of reads show an A/50% of reads show a T.
At the moment I have Illumina paired end 51bp data and some 76bp data and have mapped the reads to a reference using the maq software. Any advice oon how to do this type of downstream analysis would be much appreciated, thanks.
Lindsey
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