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Summary of Variables Used

The following are used as answers to the initial questions or for deciding which pregap stages to execute.

fofn
file_type
use_sample_names
do_qual_clip
qual_clip_interactive
screen_sv
SF or SF_com
SC or SC_com
SP or SP_com
screen_cv
CF or CF_com
screen_av
tag_alu
find_mutants
do_eba
do_sort

The following are used for default answers to the initial questions. These are only used when the associated question answer is not set.

fofn_def
file_type_def
use_sample_names_def
do_qual_clip_def
qual_clip_interactive_def
screen_sv_def
SF_def
SC_def
SP_def
screen_cv_def
CF_def
screen_av_def
tag_alu_def
find_mutants_def
WT_def

These define the locations for the programs used. They have sensible default values in the pregap script itself and so are not required to be set.

makeSCF
eba
init_exp (+ exp_args)
clip     (+ clip_args)
vector_clip
repe
trev     (+ trev_args)
getABISampleName
trace_diff

The following define the the parameters used for the vector and repeat screening programs.

vepe_svec_word_length
vepe_svec_diagonal
vepe_svec_score
vepe_svec_min_length
vepe_cvec_word_length
vepe_cvec_diagonal
vepe_cvec_score
vepe_avec_min_match
repe_repeat_file
repe_score
repe_tag_type

Used for determining the file names for the SCF and Experiment files to be created.

abi_SCF_com
alf_SCF_com
abi_Exp_com
alf_Exp_com
pln_Exp_com
scf_Exp_com
abi_Ent_com
alf_Ent_com
pln_Ent_com
scf_Ent_com

abi_filenames    (Commands to redefine the above rather
abi_samplenames   than variables themselves.)

Experiment file variables and their associated query commands. The following four are required for use by vector_clip. (The first three for sequence clipping, the fourth for cosmid vector clipping). For more information on the meaning of the two character identifiers seesection Experiment file format explained..

SF
SF_com

SC
SC_com

SP
SP_com

CF
CF_com

The following are not required, but will be added to the Experiment file during the Augment Experiment File stage if they exist. See the file $STADENROOT/doc/ExperimentFile.format for descriptions of the two letter identifiers.

CN
CN_com

CV
CV_com

SV
SV_com

DR
DR_com

DT
DT_com

MC
MC_com

MN
MN_com

OP
OP_com

TN
TN_com

ST
ST_com

PN
PN_com

PR
PR_com

SI
SI_com

SS
SS_com

EX
EX_com

AP
AP_com

CH
CH_com

QL_def

QR_def

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap_13.html