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Searching for point mutations using pregap4

Edith Schlagenhauf ediths at botinst.unizh.ch
Mon Nov 24 04:14:01 EST 2003


Hello,

we are looking for a point mutation in a BAC sequence,
thus we have quite some sequences to process.

I use a simple text database to provide the WT record
information for each sequence in the following way,
with the intention to process all data in one batch:

# BAC database 031121 ES
#ID                     ST      PR           WT
1ATG1_11_Fa             2       1       1ATG1_col_F
1ATG1_11_Fb             2       1       1ATG1_col_F
1ATG1_11_Ra             2       2       1ATG1_col_R
1ATG1_col_F             2       1       1ATG1_col_F
1ATG1_col_R             2       2       1ATG1_col_R
1ATG2_11_Fb             2       1       1ATG2_col_F
1ATG2_11_Rb             2       2       1ATG2_col_R
1ATG2_col_F             2       1       1ATG2_col_F
1ATG2_col_R             2       2       1ATG2_col_R


The tracediff processing works ok for the 1ATG1 batch
of data, but produces error messages for the 1ATG2 batch:

Fri 21 Nov 11:59:20 2003 Tracediff: Insufficient sequence overlap to
compute trace difference for 1ATG2_11_Fb.ztr.
Fri 21 Nov 11:59:20 2003 Tracediff: Insufficient sequence overlap to
compute trace difference for 1ATG2_11_Rb.ztr.
<snip>


If I process the 1ATG2 data separately as the only data,
then there is no problem with tracediff.

Is there a way to process all the data in one batch without
getting these sorts of errors?

Also, there seems to be no possibility to add WL and WR records
by way of the "Augment Experiment Files" module?

Thanks for your help in advance,
Edith Schlagenhauf




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