Jan Gielen wrote:
>When I start pregap, the first thing you need
>is a file of filenames. When I want to do interactive
>quality clipping, the program gives me always the last file
>from the file of filenames.It's like the files
>have all the same names and the program overwrights them
>every time, although they all have different names.
This could be due to having the same sample name in each of your files. As
I've now seen several cases like this I added a bit to the pregap manual
(http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap_6.html). To summarise:
It is sometimes useful to determine the experiment file names
and reading names from an ABI filename rather than the sample
named contained within it. If this is your usual form of
working then modify the abi_SCF_com, abi_Exp_com and
abi_Ent_com variables. An example would be to add the
following to your `.pregaprc' file.
abi_SCF_com='echo "${file}.scf"'
abi_Exp_com='echo "${file}.exp"'
abi_Ent_com='echo "${file}" | sed "s/ /_/g"'
This _may_ fix things for you.
James
