![]() |
|
![]() |
||||
Thread | Thread Starter | Forum | Replies | Last Post |
mergeBed -n -scores | ekimmike | Bioinformatics | 0 | 05-25-2016 01:34 AM |
Overclustered sequencing (low PF, low Q30) V2 2x250 | hcarrington | Illumina/Solexa | 5 | 07-07-2015 10:43 AM |
Wang, 'Low Cost Library Construction...': Low Concentration | MAdkisson | RNA Sequencing | 2 | 02-19-2014 02:33 PM |
quality scores, low mapped%? | chrisbala | Bioinformatics | 12 | 03-24-2010 09:42 AM |
QV scores | maggie | Bioinformatics | 1 | 01-28-2010 09:44 AM |
![]() |
|
Thread Tools |
![]() |
#1 |
Junior Member
Location: Oxford Join Date: Nov 2016
Posts: 5
|
![]()
I have just set up my very first sequencing experiment on the Next-Seq 500. It is now 45 cycles into PE sequencing, however it seems that my QC scores are a bit low. I only have a % >= Q30%: 25.2%
I have around: 280 million reads in the QC 10 bin. 25 million in the QC 20 bin 8 million in the QC 25 bin 65 million in QC 30 bin 44 million in QC 35 bin. Is this a bad result? Apologies for my stupidness, just was wondering whether data could be salvaged from this? |
![]() |
![]() |
![]() |
#2 |
Junior Member
Location: Oxford Join Date: Nov 2016
Posts: 5
|
![]()
Yes, now it has finished and the QC is only 15.2.
The machine also has a warning message on two of the lanes: camera disabled:failed to detect clusters Does this mean that the cameras are not working properly? Thanks |
![]() |
![]() |
![]() |
#3 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,698
|
![]()
Probably. You should contact Illumina tech support. They can take a look at your sequencer remotely to diagnose the problem.
If your instrument is not directly accessible over the network then you will need to send them some diagnostic files. |
![]() |
![]() |
![]() |
#4 |
Junior Member
Location: Oxford Join Date: Nov 2016
Posts: 5
|
![]()
Thanks for your reply.
Yes I will do that - unfortunately since its a weekend they cannot reply. I was thinking - if clusters are not formed in those two particular areas, would the cameras be disabled? My pooled library concentration was sufficient, so I did not anticipate any problems. Also, if the cluster density is low then I am not sure how QC would be affected.. Many thanks Last edited by ox_zoo; 11-19-2016 at 06:39 AM. |
![]() |
![]() |
![]() |
#5 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,698
|
![]()
What was the cluster density for this run?
If the run was borderline overclustered to begin with, it is possible that sequencer lost the ability to distinguish the clusters over time (they become fatter). There is also the possibility of this being some sort of a hardware issue. |
![]() |
![]() |
![]() |
#6 |
Junior Member
Location: Oxford Join Date: Nov 2016
Posts: 5
|
![]()
The cluster density for the four lanes range from 0-250k/mm2.
The lanes: Lane 1: 235 ±41 Lane 2: 237 ±38 Lane 3: 212 ±56 Lane 4: 230 ±35 I hope this helps. |
![]() |
![]() |
![]() |
#7 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 6,698
|
![]()
This run is borderline overclustered (as I recollect for NextSeq optimal cluster density is 170-220 K cluster/mm^2).
Since there is nothing to lose at this time contact tech support and see what they say. You may have to eat the cost on this one and re-run. |
![]() |
![]() |
![]() |
Tags |
illumina, next-seq, qc scores |
Thread Tools | |
|
|