aligning to the reference using CASAVA

[kjaja]

Hi,

I have exome sequencing data in zipped fastq format that I am trying to align to the reference using CASAVA. My samples have been sequenced using illumina HiSeq2000 machine, 2 x 100bp paired-end sequencing. The first step in aligning the reads using CASAVA is that I need to create a configureAlignment configuration file. This is my first time using CASAVA so I am not sure how to do that. I was wondering if there is a default setting to align the read to the reference? How to pick what options to use? Can someone provide a sample config.txt file ?

Thanks for your input

[GenoMax]

Numbers below refer to lanes. You can analyze all lanes or just one (by eliminating rest of the numbers). Put the text between the lines into "config.txt" (for non-multiplexed samples).

For CASAVA v.1.8
---------------------------------------------
ELAND_FASTQ_FILES_PER_PROCESS 4

USE_BASES Y*,Y*

12345678:ELAND_GENOME /path_to_fasta_reference_files
12345678:ANALYSIS eland_pair
-------------------------------------
Value for the "ELAND_FASTQ_FILES_PER_PROCESS" will need to be adjusted based on the RAM available on the server you are going to run the analysis on.

There are several additional parameters that you can tweak but above example should get you started.

[kjaja]

Thanks GenoMax,

In regards to the USE _BASES option, How to determine what bases to ignore when aligning the reads? Is there a rule for that?

[GenoMax]

You should not need to ignore any unless you are specifically interested in eliminating some bases from consideration at the beginning/end of the read.

Thanks GenoMax,

In regards to the USE _BASES option, How to determine what bases to ignore when aligning the reads? Is there a rule for that?

[komais]

I met a error when i use configureAlignment,such as :



config.txt is :
EXPT_DIR /mnt/eql2/liutao/trans/output/Unaligned/
USE_BASES y*,Y*
SAMTOOLS_GENOME /mnt/eql2/my_work_for_now/basic_bio_data/human_ref/hg19/hg19_pure.fa
ANALYSIS eland_pair
OUT_DIR /mnt/eql2/liutao/alignment/Aligned

when i use command line :
/illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl config_new --make

it thrown an error like

[2012-07-16 17:06:25] [configureAlignment.pl] INFO: Running self tests: 'make self_test'

output of 'make self_test':

Makefile:52: Makefiles/config.mk: No such file or directory
make: config.txt config.xml Makefile SampleSheet.csv support.txt No rule to make target `/illumina/software/CASAVA-1.8.2/share/CASAVA-1.8.2/SampleSheet.csv', needed by `Makefiles/config.mk'. Stop.


Self test command exited with error 2 (signal 0)

Investigate and fix errors, then run the command again

[2012-07-16 17:06:25] [configureAlignment.pl] Self test command exited with error 2 (signal 0)
[2012-07-16 17:06:25] [configureAlignment.pl] BACKTRACE: at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Alignment.pm line 563
Casava::Alignment::selfTest('/mnt/eql2/liutao/alignment/Aligned', 'undef') called at /illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl line 231
Died at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310.

If anybody can shed a light for me ??

[GenoMax]

Did you run the configureAlignment command while you were in this directory " /mnt/eql2/liutao/trans/output/Unaligned/"? Is there a SampleSheet.mk file in that directory?

I met a error when i use configureAlignment,such as :



config.txt is :
EXPT_DIR /mnt/eql2/liutao/trans/output/Unaligned/
USE_BASES y*,Y*
SAMTOOLS_GENOME /mnt/eql2/my_work_for_now/basic_bio_data/human_ref/hg19/hg19_pure.fa
ANALYSIS eland_pair
OUT_DIR /mnt/eql2/liutao/alignment/Aligned

when i use command line :
/illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl config_new --make

it thrown an error like

[2012-07-16 17:06:25] [configureAlignment.pl] INFO: Running self tests: 'make self_test'

output of 'make self_test':

Makefile:52: Makefiles/config.mk: No such file or directory
make: config.txt config.xml Makefile SampleSheet.csv support.txt No rule to make target `/illumina/software/CASAVA-1.8.2/share/CASAVA-1.8.2/SampleSheet.csv', needed by `Makefiles/config.mk'. Stop.


Self test command exited with error 2 (signal 0)

Investigate and fix errors, then run the command again

[2012-07-16 17:06:25] [configureAlignment.pl] Self test command exited with error 2 (signal 0)
[2012-07-16 17:06:25] [configureAlignment.pl] BACKTRACE: at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Alignment.pm line 563
Casava::Alignment::selfTest('/mnt/eql2/liutao/alignment/Aligned', 'undef') called at /illumina/software/CASAVA-1.8.2/bin/configureAlignment.pl line 231
Died at /illumina/software/CASAVA-1.8.2/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310.

If anybody can shed a light for me ??