Eland Output Explanation

Question

[Radhouane Aniba]

Hello everyone,

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 :

• Chr
• Begin
• End
• (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
• Strand

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 ?

Radhouane

Answer 1

[Istvan Albert]

Your data is in BED format the columns in question are the name of the feature (this case the read name) the score is whatever they chose to list there. The documentation (if there is one) should clear that up.

You can start analyzing this file directly since it is in an interval format that most peak callers can process.