Position less than 0 from eland sorted

[bioinfosm]

I was trying to use findpeaks on eland results using the 'separateelandsortedreads.jar' and it pointed out -ve coordinate mapped reads

R0174892        2       115     1669    54      GGTGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGGGTTAG      ggggggggWagegggfffffbfbe_ffafeffbfffffffefbeffff`b     chr16.fa        -10     R       3C35NNNNNNNNNNN 7

Anyone else seen this? What would it mean, as I never expected negative alignment coordinates

[agagne]

I noticed this recently as well. We were creating bed files, and noticed that some of our alignments started -3. I've only recently noticed this, although I do not have much experience with it. I believe it started with ELAND v2.

[kmcarr]

It is telling you that the alignment of your read is to the minus strand and it overhangs the start of your reference. The position number always indicates the left-most position of the aligned read with respect to the reference coordinate system. This position will be the location of the 3' end of the read if that read matches the minus strand of the reference. Your read has one mismatch (the red G) and 11 bases at the 3' end which have no corresponding reference, represented by the 11 N's in the match description string. (Since the numbering system includes a '0' the 11 unmatched bases start at -10.)

-10        0         10        20        30       39
 |         |         |         |         |        |
       5' - TAACCCTAACCCTAACCCTAACCCTAACCCTAACCGACC
       3' - ATTGGGATTGGGATTGGGATTGGGATTGGGATTGGCTGG
 GATTGGGTGGGATTGGGATTGGGATTGGGATTGGGATTGGGATTGG[COLOR="Red"]G[/COLOR]TGG - 5'