ELAND RNA for gene expression (error-rate)

[bioinfosm]

Hi all,

For one of our 50bp rnaSEQ run, the error profile looks very strange, with a peak of 10% error rate around base 22 for all of lane1

Is there a possible explanation for this!

[dvh]

Never seen that in quite a few RNAseq runs.

Someone added more cycle seq reagent at the wrong time, banged the machine, brief power cut, etc?

You could always N out this base position in all the fastq files, provided your chosen alignment tool can cope with N's. Shouldnt make much difference if you have 50bp reads.

[bioinfosm]

interesting, the machine stopped at that cycle and was then restarted!
But am still to find why just a single lane got affected