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Forum: Ion Torrent 05-22-2018, 09:19 AM
Replies: 37
Views: 51,956
Posted By idedios
I checked and OneTaq is compatible with uracil...

I checked and OneTaq is compatible with uracil templates. They use it for their bisulfite protocol.

Too bad OneTaq is not a HiFi enzyme. For any liquid biopsy assay where I would want to make...
Forum: Ion Torrent 05-13-2018, 04:12 PM
Replies: 37
Views: 51,956
Posted By idedios
Yeah I've been looking at alternatives too but...

Yeah I've been looking at alternatives too but it's hard to beat the sequence quality and workflow simplicity.

I'll try out a DIY ampliseq approach using NEB enzymes with some modifications:
1....
Forum: Ion Torrent 05-13-2018, 03:23 PM
Replies: 9
Views: 9,009
Posted By idedios
I currently have an S5 and noticed after the...

I currently have an S5 and noticed after the January software update it was rebranded as the GeneStudio. The internals include a single Xeon E5-1650 v4, 128GB of DDR4 RAM, a GTX 1080, and a custom...
Forum: Illumina/Solexa 12-01-2016, 02:24 PM
Replies: 0
Views: 1,128
Posted By idedios
Designing TruSeq LT Primers for IGH

Recently I created a primer design for immunoglobulin heavy chain rearrangement using Illumina TruSeq LT adapters and indexes. I'm using PCR primers from a multiplexed Sanger sequencing assay that my...
Forum: Illumina/Solexa 08-16-2016, 06:44 PM
Replies: 3
Views: 1,231
Posted By idedios
So a few things: You get fragments ranging...

So a few things:

You get fragments ranging from 0 to 250bp because those fragments are present in the final library. If you run a bioanalyzer trace you should see all the fragments with some...
Forum: Illumina/Solexa 08-11-2015, 02:19 PM
Replies: 8
Views: 3,090
Posted By idedios
Yeah this is exactly what I am using. I could ask...

Yeah this is exactly what I am using. I could ask Brad Chapman about a trimming program.
Forum: Illumina/Solexa 08-11-2015, 12:32 PM
Replies: 8
Views: 3,090
Posted By idedios
The reads are from the same fastqs. I'm just...

The reads are from the same fastqs. I'm just trying to figure out why my alignment is looking so messy when the TruSeq Amplicon stuff is supposed to have strictly sized blocks of reads. It is...
Forum: Illumina/Solexa 08-11-2015, 11:22 AM
Replies: 8
Views: 3,090
Posted By idedios
So based on a reply from biostars it looks like...

So based on a reply from biostars it looks like the BaseSpace reads have been trimmed. Now I just need to understand how they trimmed it. This is desirable since my alignment has led to the variant...
Forum: Illumina/Solexa 08-10-2015, 03:48 PM
Replies: 8
Views: 3,090
Posted By idedios
Any comments?

Any comments?
Forum: Illumina/Solexa 08-07-2015, 02:27 PM
Replies: 8
Views: 3,090
Posted By idedios
bwa mis-alignment of TruSeq Amplicon reads

http://i.imgur.com/3BCFpgu.png

I'm having the following issues using bwa mem on paired-end TruSeq Amplicon reads. I used the default settings with mem. The top sequence is from bwa mem. The bottom...
Forum: Illumina/Solexa 05-07-2015, 05:11 PM
Replies: 22
Views: 23,047
Posted By idedios
Sweet my company just got one and we'll do our...

Sweet my company just got one and we'll do our training run in a couple weeks from now. The instrument was setup and configured nearly a month ago so it's bothering to see it idle for so long.
Forum: Bioinformatics 04-16-2015, 04:46 PM
Replies: 0
Views: 1,695
Posted By idedios
Problem replacing contigs in a dbsnp vcf using Picard SortVcf

Right now I'm trying to change the contigs in the dbsnp vcf to match those of my reference genome (from 1, 2, ..., Y, MT to chrM, chr1, chr2,...)

I'm currently using JDK 1.7 u79 for compatibility...
Forum: Illumina/Solexa 01-30-2015, 04:00 PM
Replies: 0
Views: 864
Posted By idedios
Trouble installing bcbio-nextgen

So I looked into bcbio as a convenient package for onsite NGS data processing.

I install it but then it gets stuck saying the dependency ant-nodeps doesn't exist. I google search it and it looks...
Forum: Illumina/Solexa 01-12-2015, 04:03 PM
Replies: 4
Views: 6,494
Posted By idedios
I've worked with both Agilent's SureSelect QXT...

I've worked with both Agilent's SureSelect QXT workflow as well as Illumina's Nextera Rapid Capture and I found Agilent's to be quicker and easier to set up. The data was also very clean and it only...
Forum: Illumina/Solexa 01-12-2015, 03:52 PM
Replies: 4
Views: 1,653
Posted By idedios
I would suggest building your own tower PC with a...

I would suggest building your own tower PC with a couple Xeons for running bcl2fastq. Right now I'm using that type of system for demultiplexing NextSeq 500 data. It's running Fedora 21 and processes...
Forum: Illumina/Solexa 11-21-2014, 12:28 PM
Replies: 0
Views: 1,270
Posted By idedios
What variant caller should I use for Illumina TruSeq Amplicon Data?

I've been using MiSeq Reporter ever since I started using the MiSeq and it's been working pretty well for just about everything I threw at it (custom amplicon and Nextera assays). However lately I...
Forum: Illumina/Solexa 11-21-2014, 12:17 PM
Replies: 4
Views: 9,109
Posted By idedios
For MiSeq waste I throw the cartridges away in...

For MiSeq waste I throw the cartridges away in biohazardous waste and usually dump PR2 down the sink with some water. The instrument waste should be treated as biohazardous and needs to be dumped...
Forum: Illumina/Solexa 11-07-2014, 01:29 PM
Replies: 6
Views: 3,520
Posted By idedios
Some Agilent reps told me to clean the pins with...

Some Agilent reps told me to clean the pins with a brush after heavy use (like a toothbrush).
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