Difference between eland_multi.txt and eland_extended.txt

[seq_GA]

Hi,

When looking through the output files like multi and extended file produced using version 1.3, the coordinates are different in the matching chrmosome column and it is recommended to use eland_extended as the coordinates are corrected. What is meant by "correction"? Anyone know how this is being done?
Regards

[coxtonyj]

The eland_multi file contains the seed alignments of the first 32bp of the read. Positions of alignments are always expressed wrt the forward strand. This means that for alignments that hit to the reverse strand, the start position of the alignment of the read will differ from the start position of the alignment of the seed, e.g. for a 35bp read if the seed hits to position 1000 then the read hits to position 997. The eland_extended file has this correction applied.