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The '''.abi''' (or '''.ab1''') files are DNA sequence chromatogram from the sequencing machine (in ABI format). AFAICT, they come in two flavours, raw or processed, where processed means examined by a base-calling program such as [[phred]]. The file has several 'data channels', for example channel 1, 2, 3 & 4 correspond to the raw data and 9, 10, 11 & 12 corresponds to the processed data. Below is a little Perl/R hack to let you have a quick look at the data. NB: ABI.pm is here http://search.cpan.org/~malay/ABI-1.0/ABI.pm <PRE> perl -e ' use ABI; $abi = ABI->new(".../some.ab1"); @x=$abi->get_trace("A"); print join(" ", @x), "\n" ' > pingA </PRE> Repeat the above for T, C and G. Then, <PRE> perl -e ' use ABI; $abi = ABI->new(".../some.ab1"); @x=$abi->get_base_calls(); print join(" ", @x), "\n" ' > pong </PRE> and, <PRE> ## Read in data a <- as.numeric(read.table("pingA")) t <- as.numeric(read.table("pingT")) c <- as.numeric(read.table("pingC")) g <- as.numeric(read.table("pingG")) b <- as.numeric(read.table("pong")) ## Quick overview... plot(a, type='l') ## Select your range of interest (in trace points, not bases!) r <- 1000:1100 my.ylim <- range(a[r], t[r], c[r], g[r]) plot(x=r, y=a[r], type='l', ylim=my.ylim) ## lines(x=r, y=t[r], type='l', col=2) lines(x=r, y=c[r], type='l', col=3) lines(x=r, y=g[r], type='l', col=4) abline(v=b[b %in% r]+1, col=5) </PRE>
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