Contamination in my sample?

[arkal]

Hi all!

I just ran a 100bp PE human exome seq run in my lab and was looking at the fastqc results of my run. I am getting this weird pattern in the gc content distribution and was wondering is this normal for an exome run or do i have some sort of contamination? I've run an exome seq before in my lab but saw a distribution which was similar to the theoretical distribution with a shorter peak (yet, still normally distributed). The 2 peaks i'm seeing in the new run is really messing with my head as i have 24 samples all showing the same pattern!

Thanks in advance!

[arkal]

i don't know why the image is not being shown in the post... here's the link

http://www.freeimagehosting.net/79wl3

[JackieBadger]

this may help http://www.bioinformatics.babraham.a.../fastq_screen/

[arkal]

this may help http://www.bioinformatics.babraham.a.../fastq_screen/

so i tried this with a couple of my samples vs human.... i'm getting only 3% not mapping. So there is either very little or no contamination in my sample. So then what can explain the bimodal gc content distro?

[arkal]

bump

[Kath]

I've just got exactly the same with my data. What kit did you use for capture?

Cheers

Kath

[arkal]

I've just got exactly the same with my data. What kit did you use for capture?

Cheers

Kath

TruSeq exome capture.... FYI we saw it in rna seq data also!