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Forum: Sample Prep / Library Generation 10-04-2019, 02:04 AM
Replies: 10
Views: 871
Posted By torben
Most likely your RNA is free from DNA. Even...

Most likely your RNA is free from DNA. Even though the Qubit DNA assay is highly selective for double-stranded DNA, pure RNA will also give some signal, see figure 1 in...
Forum: Illumina/Solexa 06-03-2019, 03:26 AM
Replies: 3
Views: 1,366
Posted By torben
2018:...

2018: https://mkt.illumina.com/rs/600-XEX-927/images/Q218-EMEA-Prices-USD.pdf

Got nothing for 2014 though.
Forum: Ion Torrent 05-24-2019, 01:50 AM
Replies: 1
Views: 1,222
Posted By torben
There should be a templates for "Oncomine Focus...

There should be a templates for "Oncomine Focus DNA for S5" and "Oncomine Focus DNA" (at least for Torrent Suite 5.8).
Forum: Illumina/Solexa 03-11-2019, 02:46 PM
Replies: 1
Views: 860
Posted By torben
If it's not a problem to run the command twice,...

If it's not a problem to run the command twice, bbmerge (https://sourceforge.net/projects/bbmap) can do this:

bbmerge.sh in1=SAMPLE_INPUT_FORWARD.fastq in2=SAMPLE_INPUT_REVERSE.fastq...
Forum: Illumina/Solexa 01-08-2019, 01:23 AM
Replies: 1
Views: 755
Posted By torben
Yes, and yes. For the total number of cycles you...

Yes, and yes. For the total number of cycles you can run see http://emea.support.illumina.com/bulletins/2016/10/how-many-cycles-of-sbs-chemistry-are-in-my-kit.html
Forum: Ion Torrent 01-04-2019, 04:18 AM
Replies: 2
Views: 2,620
Posted By torben
All of these are common variants, see below for...

All of these are common variants, see below for allele frequencies from The 1000 Genomes Project (https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/). Your frequencies will vary depending on...
Forum: Sample Prep / Library Generation 11-14-2018, 03:53 AM
Replies: 1
Views: 998
Posted By torben
The Ion Torrent are made for blunt-end ligation...

The Ion Torrent are made for blunt-end ligation so they will not be compatible with Kapa Hyper Plus kit without some protocol modification.

The adapter sequences for Ion Torrent can be found here...
Forum: Ion Torrent 11-13-2018, 06:21 AM
Replies: 2
Views: 2,854
Posted By torben
You can add read group info to your bam-files...

You can add read group info to your bam-files using Picard's AddOrReplaceReadGroups (https://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups). You can also add it...
Forum: Illumina/Solexa 04-16-2018, 01:05 AM
Replies: 2
Views: 3,016
Posted By torben
Since it's proprietary no one outside Thermo...

Since it's proprietary no one outside Thermo really knows, but some good guesses can be found in this thread http://seqanswers.com/forums/showthread.php?t=27039
Forum: Illumina/Solexa 02-18-2018, 10:54 AM
Replies: 1
Views: 667
Posted By torben
625 according to Illumina...

625 according to Illumina https://support.illumina.com/bulletins/2016/10/how-many-cycles-of-sbs-chemistry-are-in-my-kit.html. Be avare that if you use dual indexing, there will be seven "dark" cycles...
Forum: RNA Sequencing 01-26-2018, 10:19 AM
Replies: 5
Views: 1,803
Posted By torben
From the numbers I would assume that the second...

From the numbers I would assume that the second combination (M1, M2, VS P2, P3) was done as a paired test. However, from the description of your experimental setup there's no pairing so you should...
Forum: Bioinformatics 11-13-2017, 11:30 AM
Replies: 4
Views: 1,156
Posted By torben
I don't know about any kits, but DNA can be...

I don't know about any kits, but DNA can be fragmented with reduced CuSO4
https://beng.soe.ucsc.edu/sites/default/files/project-reports/thesis_Final.pdf
Forum: Sample Prep / Library Generation 10-12-2017, 02:11 AM
Replies: 10
Views: 2,514
Posted By torben
For a way to create TruSeq adapters with UMI at...

For a way to create TruSeq adapters with UMI at the end see Kennedy SR, et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat Protoc. 2014 Nov;9(11):2586-606. doi:...
Forum: Ion Torrent 09-25-2017, 03:04 AM
Replies: 1
Views: 3,999
Posted By torben
You can use fusion PCR primers (ie. primers with...

You can use fusion PCR primers (ie. primers with the A and P1 sequences included) directly in the first PCR (or in a second PRR run if you prefer):...
Forum: Illumina/Solexa 09-25-2017, 02:41 AM
Replies: 6
Views: 1,919
Posted By torben
The easiest way to scale down is to reduce all...

The easiest way to scale down is to reduce all the volumes in the reaction. I usually use half the volumes given in Illumina's protocol, and I have collaborators who only use a quarter of the volume....
Forum: Ion Torrent 08-03-2017, 03:42 AM
Replies: 1
Views: 2,854
Posted By torben
IIRC the probe binds within the P1 adapter,...

IIRC the probe binds within the P1 adapter, that's why the kit is not compatible with the use of fusion primers with truncated P1.
Forum: Sample Prep / Library Generation 07-03-2017, 02:26 AM
Replies: 12
Views: 10,923
Posted By torben
A qucik look at the SDS...

A qucik look at the SDS (https://www.beckmancoulter.com/wsrportal/ajax/viewFile?documentId=45481385 ) confirms that they do.
Forum: Sample Prep / Library Generation 05-29-2017, 04:20 AM
Replies: 1
Views: 1,207
Posted By torben
Both serial (or serial to usb) cable, priming...

Both serial (or serial to usb) cable, priming station, and vortexer/vortex adapter is available as spare parts but will cost a lot more than $600. I don't know if you can get a license separately,...
Forum: Illumina/Solexa 04-27-2016, 05:36 AM
Replies: 3
Views: 1,835
Posted By torben
Hi, the extra peak is probably due to...

Hi,

the extra peak is probably due to overamplification which can give you ssDNA that migrates slower than dsDNA. See e.g. slide 30 here:...
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