[greigite]

comparison of SE and PE sequences

Hi all
I put together a comparison of SR and PE sequences to get a quick look at regions of sequence similarity. Thought it might be useful for others (let me know if you spot errors). As far as I can tell, the SR and PE read 1 sequencing primers are identical, as are the SR and PE adapters with the T overhang. Seems to me that given this, it should be fine to run a PE library on an SR flowcell using SR reagents. Comments?
All the sequences are from the Bentley et al. nature paper supplementary info last year.

[greigite]

Perhaps the sequences are shown in Figure 2 and table S3 of this paper by Craig et al (http://www.nature.com/nmeth/journal/...th.1251.html)? I notice one of the authors has an Illumina affiliation and the paper describes 6 bp error corrected tags. Of course, they don't tell you outright which ones are the best but my guess is the 13 tags showing less than 2-fold difference in index frequencies between runs (Fig 2).

Hi,

Has anyone got the multiplex oligo sequences that Illumina use in their Multiplex (12-plex) kits? (And their concentrations if they're known.)

[hilahg]

yes it helps, thank you

[sci_guy]

Do pages 17 - 20 of this help?

[hilahg]

the figure came out wrong... I hope you can still understand my question above....

[hilahg]

which adapters to use

Hi all,
I have a question:
I've prepared a cDNA library for solexa (double stranded) with 5' end after enzymatic cleavage by MMEI (see below). I would like to perform a single read from 5' (the left side with the MME sticky end). GEX2 adapter fits this site. My question is which adapter do I need for the 3' side to perform a single read of the 5' side (left side)?

5'_________? 3'
adapter Gex 2 3'___________
(MMEI side) which adapter on this side?

Can anyone answer this???

[danielfortin86]

Adapter sequence

i know that the overhanging T is used to ligate with the added A from the DNA library, but thy is there a one base pair overhang on the other side? If you see how the sequence anneal there is an overhang on both ends. Both adapter sequences are 33 bases. If you only wanted the T overhang, why wouldn't you have 32 bases on one strand and 33 on the strand with the T overhang?

[ECO]

Hey Brent,

Nice to have you, thanks for being willing to share with the community. I'm sure everyone would appreciate any info you have.

[graveley]

Hi,

I run the site you got the sequences from and am happy to see that you have posted the info here as well. I will attempt to keep the list up to date as new sequences are released. If there is any additional info you would like, let me know and I'll post it if possible.

Cheers,

Brent

[dvh]

Hi all,

Thanks for the technical details on this. Anyone got some information about bioinformatics on adapter contamination detection and removal. I tried using adapter sequences with eland to check for contamination, but less than 1% reads aligned. I expected more as less than 10% reads aligned to actual reference.

I know of a file one can specify in GA pipeline, to exclude sequences -- could someone point more details on the same? (i tried bioinformatics thread, but did not hear back )

thanks!

novoalign has 5' and 3' removal of adapter sequences prior to alignment. works well.
david

[breakt1000]

Multiplex (12-plex) Illumina Adapter/Primer Sequences

Hi,

Has anyone got the multiplex oligo sequences that Illumina use in their Multiplex (12-plex) kits? (And their concentrations if they're known.)

[bioinfosm]

Hi all,

Thanks for the technical details on this. Anyone got some information about bioinformatics on adapter contamination detection and removal. I tried using adapter sequences with eland to check for contamination, but less than 1% reads aligned. I expected more as less than 10% reads aligned to actual reference.

I know of a file one can specify in GA pipeline, to exclude sequences -- could someone point more details on the same? (i tried bioinformatics thread, but did not hear back )

thanks!

[berthasalco]

Hello there,

first at all, i want to thank you to all to coperate to give us the sequence of the GEX 1 and 2 adapters and primers for the tag profilling with DpnII , but

does anybody know at which concentration are they used??? The Illumina protocol does not give concentrations. According to the Invitrogen LongSAGE protocol the double stranded adapters have a concentration of 40 ng/ul and 1.5 ul are used for one ligation reaction

thanks a lot,
BS

[monad]

mRNA-seq adapters

The sequences above are really helpful. Does anyone also have the sequences for mRNA-Seq? This would be really great!!!

mRNA-seq kit uses PE adaptors, and read 1 primer is same as genomic DNA primer for single read sequencing. If you have a PE sample ready, but whatever the reason wants single end sequencing, do that just like for SR sequencing. Done that many times.

[Joanne Ho]

I use PE-adapter to mRNA-seq, it can work properly.