[GenoMax]

@melop: It is still not clear if you have talked with the facility about your data/concerns and what the result of that conversation was? Do you know if they contacted Illumina tech support about this run?

Based on your post in #29 it seems that other 6 lanes on this flowcell were very close to acceptable spec (Illumina spec only specifies 75% bases > Q30 for 2 x 150bp, which seems to refer to entire sequence output from that flowcell).

It is certainly possible that Illumina refused to provide free replacements. As with any customer service issue the kind of response one gets (in this case free replacements) may entirely depend on the support person you reach.

Ultimately your result may be due the characteristic of the library. A re-run may produce a very similar result. Only option then would be to remake the library and try again.

[melop]

@melop: It is still not clear if you have talked with the facility about your data/concerns and what the result of that conversation was? Do you know if they contacted Illumina tech support about this run?

Based on your post in #29 it seems that other 6 lanes on this flowcell were very close to acceptable spec (Illumina spec only specifies 75% bases > Q30 for 2 x 150bp, which seems to refer to entire sequence output from that flowcell).

It is certainly possible that Illumina refused to provide free replacements. As with any customer service issue the kind of response one gets (in this case free replacements) may entirely depend on the support person you reach.

Ultimately your result may be due the characteristic of the library. A re-run may produce a very similar result. Only option then would be to remake the library and try again.

Yes, they said they will rerun if illumina replaces the reagent for them. They did not say what happens if not. But from the message they seemed to imply that rerunning is contingent upon their success in the negotiations. They stopped replying to our emails after that.

[GenoMax]

That is unfortunate. If they don't intend to re-run your samples for free (due to not getting free replacements) then they should have informed you.

Since they made the libraries this is one of those tough situations (for them, in terms of cost) where they should at least do something to retain your business (either re-run the current libraries to see if the problem recurs or remake the libraries for free but then charge you for running them, only if the new data looks good).

[NextGenSeq]

Dear all. I'm an end user. Recently we got 2 HiSeq 4000 lanes from a local sequencing facility (150bp x 2 reads), PCR-free gDNA libraries made at the same facility. The quality looks quite bad, especially in read 2, only 60% and 70% of bases >Q30, which doesn't pass the Illumina specs. In this case, is it a common practice for the facility to redo the sequencing for us? We ask because it sounded like they don't want to redo it for us... How about the policy at your sequencing core?

Illumina will almost always send replacement reagents if you use a small amount of spike-in PhiX sequenced with your library AND the PhiX did not give good sequencing results. If the PhiX gives good sequencing results the problem is the library not the instrument. If both give poor results it is likely an instrument or reagent problem.

If the sequencing facility did not do this they are amateurs and you shouldn't use them again.