Read results explanation?

[arkilis]

Read 1 Read 2
Lane Aligned Error Aligned Error
1 0.94% 0.19% 0.92% 0.42%
2 0.96% 0.19% 0.94% 0.38%
3 0.95% 0.19% 0.94% 0.39%
4 0.95% 0.18% 0.94% 0.40%
5 0.97% 0.17% 0.87% 0.52%


Sorry to bother again, is "Algined" means only 0.xx% has been aligned? And "Error" means 0.xx% went wrong?

[GenoMax]

What alignment program (or pipeline) is this output from?

[arkilis]

Thank you again GenoMax!

I am not quite sure, it might be next gen pipeline, totally new to the bioinformatics.

Thanks,

[GenoMax]

It would be better to provide some additional information as to what was done to get this output. In a literal sense what you are interpreting is probably right but with no additional context I am hesitant to concur.

BTW: Those would be awfully low alignment percentages, if the numbers are real percentages (out of 100%).

[arkilis]

Thanks! What I know about the program is "Illumina RTA 1.17.21.3". I probably need to ask the people who runs the pipeline for more details.

[arkilis]

It would be better to provide some additional information as to what was done to get this output. In a literal sense what you are interpreting is probably right but with no additional context I am hesitant to concur.

BTW: Those would be awfully low alignment percentages, if the numbers are real percentages (out of 100%).

Thanks! What I know about the program is "Illumina RTA 1.17.21.3". I probably need to ask the people who runs the pipeline for more details.

[GenoMax]

Is this output from a HiSeq or a MiSeq run?

[arkilis]

Is this output from a HiSeq or a MiSeq run?

Sorry for confusion. It is Hiseq.

[Tom Barker]

My first thought was that % aligned corresponds to the percentage of reads that aligned to phiX (hence why it seems low). Often 1% phiX is spiked into a lane on a HiSeq or MiSeq and is used to calculate an error rate. RTA is real time analysis software which as the name suggests analyses the data while the flow cell is running. This was just my first thought when I read your post so may be completely wrong as I am not a bioinformatician.

[GenoMax]

My first thought was that % aligned corresponds to the percentage of reads that aligned to phiX (hence why it seems low). Often 1% phiX is spiked into a lane on a HiSeq or MiSeq and is used to calculate an error rate. RTA is real time analysis software which as the name suggests analyses the data while the flow cell is running. This was just my first thought when I read your post so may be completely wrong as I am not a bioinformatician.

That is a reasonable (and possible) explanation.

arkilis: Check with the folks who ran the initial analysis to see if that is true.

[arkilis]

Sorry, Still not get answer from the guy who is in charging this.. Definitely I will post it once got replied.

[arkilis]

My first thought was that % aligned corresponds to the percentage of reads that aligned to phiX (hence why it seems low). Often 1% phiX is spiked into a lane on a HiSeq or MiSeq and is used to calculate an error rate. RTA is real time analysis software which as the name suggests analyses the data while the flow cell is running. This was just my first thought when I read your post so may be completely wrong as I am not a bioinformatician.

Exactly like what you said, Genius!

See the link for more detailed info:

http://res.illumina.com/documents/products/technotes/technote_phixcontrolv3.pdf