Are Solexa GAPipeline v.1.0 ELAND results realignable with new v.1.4 ELAND module?

marlei · 10-12-2009, 03:55 AM

Hi!

I have an old project of Solexa GA runs that should be compared to new Solexa runs. The old sequence data was analysed with Solexa GAPipeline v.1.0.

Data analysis files available from the old analysis are only these ELAND Alignment results:
s_*_sequence.txt
s_*_eland_result.txt

Is it possible to realign old results, that is, use these as an input to new Solexa GA Pipeline v.1.4 ELAND_standalone.pl? And if so, how? It seems some conversions of the input files are necessary...

Best regards

Maria

marlei · 10-15-2009, 06:51 AM

I managed to solve the compatibility problem with help from Illumina Tech. Support.

Solexa GAPipeline v.1.0 results s_*_sequence.txt (fastq format input files) need to be modified as follows:

perl -pe 's/^\@(.*)$/\@\1\#0\/1/' | perl -pe 's/^\+(.*)$/\+\1\#0\/1/' | perl -pe 's/HWI-EAS/HWI_EAS/'

Note that also ELAND v.1.4 results should be modified with
perl -pe 's/HWI-EAS/HWI_EAS/'
This will satisfy the v.1.4 ELAND_standalone.pl.

Invoke example:
/Pipeline/GAPipeline-1.4.0/bin/ELAND_standalone.pl -if s_4_sequence-converted.txt -it fastq -eg ../../Genomes/Hg19_squashed/ -op realigned-4

--
Best regards

Maria

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10-12-2009, 03:55 AM	#1
marlei Junior Member Location: Helsinki Join Date: Oct 2009 Posts: 5	Are Solexa GAPipeline v.1.0 ELAND results realignable with new v.1.4 ELAND module? Hi! I have an old project of Solexa GA runs that should be compared to new Solexa runs. The old sequence data was analysed with Solexa GAPipeline v.1.0. Data analysis files available from the old analysis are only these ELAND Alignment results: s__sequence.txt s__eland_result.txt Is it possible to realign old results, that is, use these as an input to new Solexa GA Pipeline v.1.4 ELAND_standalone.pl? And if so, how? It seems some conversions of the input files are necessary... Best regards Maria

10-15-2009, 06:51 AM	#2
marlei Junior Member Location: Helsinki Join Date: Oct 2009 Posts: 5	I managed to solve the compatibility problem with help from Illumina Tech. Support. Solexa GAPipeline v.1.0 results s__sequence.txt (fastq format input files) need to be modified as follows: perl -pe 's/^\@(.)$/\@\1\#0\/1/' \| perl -pe 's/^\+(.*)$/\+\1\#0\/1/' \| perl -pe 's/HWI-EAS/HWI_EAS/' Note that also ELAND v.1.4 results should be modified with perl -pe 's/HWI-EAS/HWI_EAS/' This will satisfy the v.1.4 ELAND_standalone.pl. Invoke example: /Pipeline/GAPipeline-1.4.0/bin/ELAND_standalone.pl -if s_4_sequence-converted.txt -it fastq -eg ../../Genomes/Hg19_squashed/ -op realigned-4 -- Best regards Maria