First-of-pair strand color

[Nicolas R]

Hi,

I've strand-specifc data (Illumina 2x50bp dUTP). In IGV, what is the meaningful of the colors ? red = anti-sens  and blue = sens ?

Thanks,

N.

[Jacob Silterra]

The color indicates the first-in-pair read strand. Red is positive strand, blue is negative.

-Jacob

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Jacob Silterra
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Broad Institute

[Nicolas R]

Where did you find this infos ?

[Jacob Silterra]

I don't believe it's in the user documentation, that would be a good thing for us to include.

The color rendering is in AlignmentRender.getAlignmentColor, case FIRST_OF_PAIR_STRAND. Source at https://github.com/broadinstitute/IGV/blob/master/src/org/broad/igv/sam/AlignmentRenderer.java

-Jacob

[Nicolas R]

I ask that because Jim Robinson post on seqanswers that :

red = neg strand (first read of the pair is no the neg strand)
blue = pos strand
grey = pair information not available, so "first of pair" is undefined

http://seqanswers.com/forums/showthread.php?t=22358&highlight=first-of-pair

So I don't know now :p

[yvan]

Hello
I thought red is for shorter than expected insert and blue longer then expected
from the IGV documenation:

GV colors paired-end alignments whose inferred insert size is larger than expected or whose mate read is ali chromosome. A read with a mate aligned to a different chromosome is color-coded to identify the other chrom chromosome color legend is on the Alignments tab of the Preferences window (/software/igv/?q=Preferences#Alignme

IGV uses color coding to flag anomalous insert sizes.

Blue is for inserts that are smaller than expected. That is, the inferred insert size on the reference gen expected given the actual insert size.

Red is for inserts that are larger than expected. That is, the inferred insert size on the reference geno expected given the actual insert size.

Or is this obsolete?

yvan

[Jim Robinson]

Hi,

Coloring by insert-size is the default,  but there are many other options.  Right-click to see the full list.   

It appears that my answer on seqanswers is backwards,  blue is the neg strand color and red positive.  In any event,  interpreting first-of-pair read strand is very dependent on your library prep,  which IGV cannot know about,  so the important information here is that the pairs are colored by the strand of first-in-pair,  red for one strand, blue for the other, and grey for unknown (unpaired mate or mate not mapped).  

Jim