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Forum: Illumina/Solexa 04-25-2018, 04:16 AM
Replies: 6
Views: 2,716
Posted By jov14
Thanks, I missed those options somehow, when I...

Thanks, I missed those options somehow, when I was looking for them earlier...
Converning the use of primers with TruSeq kits, We are actually mostly using NEB library prep kits which are Trueseq...
Forum: Illumina/Solexa 04-24-2018, 08:30 AM
Replies: 6
Views: 2,716
Posted By jov14
Creating Custom dual index primers for Illumina Seqeuncing

I need help (or tips) for creating my own indexing-primers for Illumina seqeuncing (TrueSeq-compatible):

It seems to me that I could simply devise my own index primers based on the Trueseq adapter...
Forum: Bioinformatics 01-13-2017, 12:09 AM
Replies: 53
Views: 38,405
Posted By jov14
@Brian Bushnell Thanks a lot. Now BBnorm...

@Brian Bushnell
Thanks a lot. Now BBnorm completed successfully.
Forum: Bioinformatics 01-12-2017, 05:33 AM
Replies: 53
Views: 38,405
Posted By jov14
A question reagarding the partitioning option of BBnorm

Hi,
I want to preferentially assemble the genome of a low abundant community member from a metagenome, so I am interested in the partitioning option of BBnorm.

I have some questions on how to...
Forum: Bioinformatics 01-12-2017, 05:04 AM
Replies: 0
Views: 1,765
Posted By jov14
Partitioning huge paired-end datasets with the khmer suite

The khmer suite has a workflow for partitioning reads based on graph-connectivity, which I want to test for a specific (huge) paired-end dataset.

However, from the documentation, I am not sure how...
Forum: Illumina/Solexa 01-06-2016, 11:21 PM
Replies: 10
Views: 8,612
Posted By jov14
@carladosanjos: It worked fine. The quality was...

@carladosanjos: It worked fine. The quality was not worse than for any normal run. It's definitevely worth giving it a shot instead of throwing away the cartridge.
Forum: Bioinformatics 08-13-2015, 04:29 AM
Replies: 4
Views: 4,250
Posted By jov14
Thanks for your answer and suggestion! After...

Thanks for your answer and suggestion!
After Iposted this "problem" and had some more time to think again it came back to me:
Since, as you say, Diginorm only starts to exclude reads if ALL kmers...
Forum: Illumina/Solexa 08-13-2015, 01:14 AM
Replies: 3
Views: 5,428
Posted By jov14
Thanks for the reply. So as i understand it, the...

Thanks for the reply. So as i understand it, the FASTQC-plot shows two opposide sides of my flow cell in part only, in my case?

I'll also try the illumina customer support. However, at least...
Forum: Illumina/Solexa 08-12-2015, 08:48 AM
Replies: 3
Views: 5,428
Posted By jov14
Illumina MiSeq-run: Bad quality per tile. How should i interpret this fastqc-image?

I recently got very bad sequencing results from a Miseq Illumina run. The average Sequence qualities declined very early, leading to low read lengths after quality clipping.

When I looked at the...
Forum: Bioinformatics 08-12-2015, 07:40 AM
Replies: 4
Views: 4,250
Posted By jov14
kmer size and coverage cutoff for digital normalization using the khmer suite

Hi,

I want to use digital normalization on a set of single cell sequencing data as well as metagenomic date from low complexity communities. I'm probably missing some really obvious point, but I...
Forum: Illumina/Solexa 04-28-2015, 08:53 AM
Replies: 7
Views: 2,758
Posted By jov14
Hi, everyone. while trying to figure out how...

Hi, everyone.
while trying to figure out how to install which boost library, I simultaneously tried the alternative approach of installing via the Illumina-supplied rpm-package using the...
Forum: Illumina/Solexa 04-28-2015, 07:10 AM
Replies: 7
Views: 2,758
Posted By jov14
I have boost version 1.54 installed, which seems...

I have boost version 1.54 installed, which seems to be the newest version of boost in the official Ubuntu repositories.
So I guess that means I should download the most current version of boost...
Forum: Illumina/Solexa 04-28-2015, 06:44 AM
Replies: 7
Views: 2,758
Posted By jov14
Thanks a lot! I was sure I had libxml2...

Thanks a lot!
I was sure I had libxml2 installed, but i seem to have been mistaken...
Configure now completed without errors. However, now I run into the following errors during "make" at 51%
[...
Forum: Illumina/Solexa 04-28-2015, 05:55 AM
Replies: 7
Views: 2,758
Posted By jov14
problems configuring installation of Bcl2fastq

Hi,
I want to install Bcl2fastq on my system running Ubuntu 14.04.2 LTS. I have admin rights.

However the configure step always aborts with an error.

After running configure I first ran into...
Forum: Illumina/Solexa 04-24-2015, 01:12 AM
Replies: 10
Views: 8,612
Posted By jov14
Ok, thanks. It's a great relief to know that this...

Ok, thanks. It's a great relief to know that this cartridge is not clearly lost. It'll be a while till we may use this specific (150 cycle) cartridge, but when we do, I'll try to remember to post...
Forum: Illumina/Solexa 04-23-2015, 06:45 AM
Replies: 10
Views: 8,612
Posted By jov14
refreeze thawed reagent cartridge for Miseq (v3)

Hi everyone,
We accidentally thawed the wrong type of reagent cartrige for loading samples onto our Illumina MiSeq machine. We noticed only after the cartrige was completely thawed, that it...
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