AB1
| File format | AB1 |
|---|---|
| Data type | basecall |
| Used by |
Full text description
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
perl -e '
use ABI;
$abi = ABI->new(".../some.ab1");
@x=$abi->get_trace("A");
print join(" ", @x), "\n"
' > pingA
Repeat the above for T, C and G. Then,
perl -e '
use ABI;
$abi = ABI->new(".../some.ab1");
@x=$abi->get_base_calls();
print join(" ", @x), "\n"
' > pong
and,
## 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)
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