[BiO BB] Base Trimming by PHRED
yunlee at bme.jhu.edu
Thu Jun 19 17:41:39 EDT 2003
I have been calling bases from ABI files using the following command.
phred -trim_alt "" -trim_fasta -id <ABI directory> -sd <fasta directory>
-qd <qual directory>
This way, phred trims off low quality parts of the sequence. If I were to
omit the first two flags, then I get a longer sequence containing the low
quality parts of the sequence.
After trimming, phred adds the trim information to the header line. For
>CF-500-2-A04-T7.ab1 1015 0 1015 ABI trimmed
According to the phred documentation, the first number(1015) is the number
of bases called by phred, the second number(0) is the number of bases
trimmed, and the third number(1015) is the number of bases remaining after
My problem is that although trimming is occuring, the numbers on the
header line are not appearing properly. I always get them in the form
some_number 0 some_number
Thus, it always seems like no bases were trimmed. However, I know they
were trimmed since I get a longer sequence when I call bases on the same
sequence file without the trimming options.
Does anybody know what is going on?
I am running phred version 0.020425.c on AIX 5.1 on an IBM p690 machine.
Any advice would be greatly appreciated.
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