Eland alignment file

[Anna]

Hi
I am just wondering that anyones knows how to convert eland
alignment files(export/sorted) to eland.extended.txt or
eland.results.txt.
Any suggestions are appreciated.
thanks

[Lingsheng Dong]

Hi, Anna,
I remember the extended.txt contains all alignments, while export.txt only contain unique alignment. So I think you can not convert export to extended. But I believe you can convert extended to export. A few weeks ago, I want to do so, but Illumina support could find the script to to the work. So I have to use bowtie instead of eland to find the unique alignment, because I don't have the raw sequence data from CASAVA. Please correct me if it is wrong.
Best,
Lingsheng
 

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[Anna]

Hi Lingsheng,
Thanks for response.
As far as I know s_N_export.txt file contains the results of alignment
of all reads in the lane. This file has a line for every read, not
just those that pass filtering and s_N_sorted.txt is similar to
s_N_export.txt, except it contains only entries for reads which pass
filtering and have a unique alignment in the reference. These are
sorted by order of their alignment position.
Regards
Anna

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