ask Peter Marquardt about access to the machine where analysis should be done. In my case: directory: /project/solexb name: solexb
ask Wei Chen what is the best version of the analysis software at the moment and what the pathway to it is. On the moment of text preparation the best version was 0.2.0 and pathway was: /project/solexa/src/SolexaPipeline-0.2.0
Login procedure
for short runs
login on molgix machine with your name and Unix password: [program: PuTTY · host name: molgix.molgen.mpg.de · port: 22 · protocol: SSH];
connect to the machine where analysis will be performed ('hurtz' in my case) with the username from Pefer ('solexb' in my case):
for long runs
login on molgix machine with your name and Unix password;
check, that ther is no old screen-sessions:
organize screen-session:
connect to the machine where analysis will be performed:
--- start some long analysis ---
create virtual screen:
--- now it is possible to log out ---
login on molgix machine again;
run virtual session on the screen:
Transfer sequencing data (images)
Transfer folder YYMMDD_SLXA-EAS12_NNNN (070216_SLXA-EAS12_0034/' ~450Gb) to USB-hard disk (~1 day)
login as 'solexb';
go to the analysis directory:
create symbolic link to the current Solexa_Sequence_Analysis_Package:
organize 'data' directory:
download images (folder YYMMDD_SLXA-EAS12_NNNN) in the 'data' folder (~1 day): in this example data were transferred in 'harddisk-20070220/070216_SLXA-EAS12_0034/', but it not necessary to create an additional folder, so '070216_SLXA-EAS12_0034/' would be better
prepare folders (folder 'Genome' for fasta-files; folder 'mouseGenome' for 2-bits-per-base format files) for the reference genome:
download reference genome
prepare 2-bits-per-base format genome files
unpack the *.tar.gz genome archive:
a lot of folders will be organized with 1-2 files per folder:
prepare 2-bits-per-base format files:
check 2-bits-per-base format files:
remove folders with *.fa files:
Test analysis
Test analysis takes one tile (from 200) in one channel (from 8). In this example tile '50' from channel '4' was selected (parameter --tiles=s_4_0050). Test analysis is performed to check software and estimate the quality of the sequencing quickly.
Goat-run
perform test Goat-run:
create Goat-make-file:
check that a new Firecrest-folder appears in the Data-folder:
in my case it was: C1-27_Firecrest1.8.26_06-03-2007_solexb.2
perform Firecrest-run -- go to Firecrest-folder and run 'make':
check, that 'int-file' appears (in this case: s_4_0050_int.txt) in Firecrest-folder:
perform 'Bustard' run - go to Bustard-folder and run 'make':
check, that "seq-file" appeared in Bustard-folder: (in this case: s_4_0050_seq.txt):
check, that the content of the s_4_0050_seq.txt is similar to what you expect to obtain from the sequencing.
Sequence-alignment (GERALD' run)
Prepare config.txt file and put it in the /project/solexb folder:
perform 'GERALD' run:
the program perform "make self_test" automatically. If everything OK, go to the GERALD-directory and run "make":
check, that ELAND-results in the "s_4_eland_result.txt" file look acceptable.
Second-generation sequencing
URL: http://seq.zbio.net
e-mail: soldatov@molgen.mpg.de
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Second-generation sequencing > Analysis
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