I am working on the analysis of some Chip-Seq data for a biologist, and she just provided me with the eland alignments, but it is not looking as the data I used to download from GEO, even if they are both in BED format.
I used to have alignment file showing : Chr, Start, Eng, the tag sequence, score and Strand.
But opening these data I found this :
- (Something) looking like this : 30F94AAXX:4:035:1560:1586
- (Something) looking like values going from 0 to 2 I guess it is the number of mismatches
I don't understand the 4th and 5th columns ! what are they corresponding to ? Also I am using QuEST to analyze these Chip-Seq data so I am thinking about using galaxy to extract genomic sequences from coordinates and create another BED file but I don't know if this is the right thing to do giving the mismatches column.
Any explanation ?