Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

Redo the read-filtering process
Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix D Advanced Topic: Primary Analysis
Primary analysis workflow D
Redo the read-filtering process by trimming the last several bases:
1. Go to the following location inside the JobID folder:
$sampleJobFolder/postPrimerSetPrimary
2. Enter the following modification in the parameters.ini file:
read.length={your desired read.length}
3. Enter the following command:
jprimaryanalysis.sh --ini=parameters.ini
Check the completion of primary analysis
The summary of the primary analysis results is written in a “.stats”
file. This file is called:
{run.name}_{sample.name}_F3.stats
for F3 tag analysis
or
{run.name}_{sample.name}_R3.stats
for R3 tag analysis.
The file is located in:
/data/results/{instrument.name}/{run.name}/{sample.name}
/results/primary.[17-digit timestamp]/reads/
Example of a “.stats” file:
# Mon Mar 31 22:28:42 2008
/share/apps/corona/bin/filter_fasta.pl --noduplicates -output=/data/results/Solid/Solid_20080310_1/DH10B/result
s.01/primary.20080328155539890 -name=Solid_20080310_1_DH10B_
--tag=F3 --minlength=35 -mask=11111111111111111111111111111111111
--prefix=T
/data/results/Solid/Solid_20080310_1/DH10B/jobs/postPrim
erSetPrimary.847/rawseq
# Cwd: /home/pipeline
# Title: Solid_20080310_1_DH10B_
Totals (2357 p): 81935898 / 90577909 (90.5%):
(Duplicates: 8085 [0.0%] (TooManyErrors: 8633926 [9.5%]
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