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Search: Posts Made By: MadsAlbertsen
Forum: Illumina/Solexa 12-18-2013, 02:39 AM
Replies: 16
Views: 6,930
Posted By MadsAlbertsen
Sure. I've attached them here. You can find the...

Sure. I've attached them here. You can find the protocol we use here: http://midasfieldguide.org/

rgds
Mads Albertsen
Forum: Bioinformatics 10-24-2013, 02:07 AM
Replies: 3
Views: 1,101
Posted By MadsAlbertsen
Thanks for the suggestions. I have been trying...

Thanks for the suggestions. I have been trying some of your Ray related projects :). Cortex seem to be in the direction I was thinking of.



I want to use multiple related metagenome samples to...
Forum: Bioinformatics 10-23-2013, 02:08 AM
Replies: 3
Views: 1,101
Posted By MadsAlbertsen
De novo assembly utilizing abundance information from multiple samples

In my lab we do loads of metagenome sequencing and assembly to recover complete genomes from environmental samples. To bin the genomes we use abundance information from multiple related samples and...
Forum: Illumina/Solexa 10-14-2013, 06:10 AM
Replies: 9
Views: 2,418
Posted By MadsAlbertsen
It seem to have been a tile failing that caused...

It seem to have been a tile failing that caused the processing of the images to stop. The Illumina tech support was able to disable the specific tile and after a restart of RTA we seem to be up and...
Forum: Illumina/Solexa 10-13-2013, 03:18 AM
Replies: 9
Views: 2,418
Posted By MadsAlbertsen
OK. Thanks for the fast answer - we'll give it a...

OK. Thanks for the fast answer - we'll give it a go.

rgds
Mads
Forum: Illumina/Solexa 10-13-2013, 01:01 AM
Replies: 9
Views: 2,418
Posted By MadsAlbertsen
Seems like we just got the same problem. Huge...

Seems like we just got the same problem. Huge amounts of raw data filling up the drives without being processed.

Did it work to just restart the RTA?

rgds
Mads Albertsen
Forum: Illumina/Solexa 09-22-2013, 11:02 PM
Replies: 4
Views: 2,458
Posted By MadsAlbertsen
Nice to see that you got it to work. We use the...

Nice to see that you got it to work. We use the new loading reccomendations of 20 pM. However it is very difficult to estimate the right concentration of the samples due to the differences in insert...
Forum: Illumina/Solexa 09-18-2013, 10:12 AM
Replies: 4
Views: 2,458
Posted By MadsAlbertsen
We just did some stranded RNAseq libraries with...

We just did some stranded RNAseq libraries with MiSeq v3 kits.

Worked perfectly. 1340 k/mm^2 density and 32M reads (29M passed).

rgds
Mads
Forum: Illumina/Solexa 09-18-2013, 10:06 AM
Replies: 2
Views: 1,234
Posted By MadsAlbertsen
You would be perfectly fine with 5% of a HiSeq...

You would be perfectly fine with 5% of a HiSeq lane for a PE library and 1% for a MP library.

100x coverage should be fine. You can calculate the needed amount of sequence as:

100 x 4.7 mbp =...
Forum: Illumina/Solexa 09-13-2013, 03:18 AM
Replies: 16
Views: 6,930
Posted By MadsAlbertsen
You basically have to test it on your samples....

You basically have to test it on your samples. The theoretical evaluation of the "best" primersets are in our experience worth very little.

In all new environments we test V1-3, V3-4 and V4 to see...
Forum: Introductions 08-23-2013, 04:32 AM
Replies: 3
Views: 1,479
Posted By MadsAlbertsen
See this blog: ...

See this blog:

http://thegenomefactory.blogspot.dk/2012/11/tools-to-merge-overlapping-paired-end.html

We are currently using FLASH - which works nicely.

rgds
Mads
Forum: Illumina/Solexa 08-23-2013, 01:30 AM
Replies: 25
Views: 7,820
Posted By MadsAlbertsen
We do not see that dramatic error rate in the...

We do not see that dramatic error rate in the merged sequences.

I've attached a quick plot of how the quality score usually looks after merging.

rgds
Mads
Forum: Metagenomics 08-22-2013, 11:15 AM
Replies: 1
Views: 1,275
Posted By MadsAlbertsen
Genome extraction from metagenomes

Hi all,

I've made a step-by-step guide on how to extract genomes from metagenomes.

The guide uses the real data we used in the paper...
Forum: Illumina/Solexa 08-22-2013, 09:04 AM
Replies: 25
Views: 7,820
Posted By MadsAlbertsen
Why not 2x301 on v2 kits?

If you have a bunch of old kits you can just hack the 2x250bp v2 kits to run 2x301 bp.

It works quite nice - we have been sequencing full V1-3 16S on MiSeq since April.

You can see how we do...
Forum: Illumina/Solexa 06-20-2013, 10:51 PM
Replies: 4
Views: 806
Posted By MadsAlbertsen
If you want closed genomes de novo you could also...

If you want closed genomes de novo you could also just use the Illumina Nextera Mate-pair protocol. In our experience it works great and usually results in a single chromosome.

However, the...
Forum: Bioinformatics 01-23-2012, 12:52 AM
Replies: 4
Views: 660
Posted By MadsAlbertsen
Most assemblers have a function to obtain the...

Most assemblers have a function to obtain the average coverage for each contig - it's a long time since I've used ABySS so I can't remember if it has an output contig coverage option.

Otherwise...
Forum: Bioinformatics 01-22-2012, 05:21 PM
Replies: 4
Views: 660
Posted By MadsAlbertsen
The first thing I do after an assembly is always...

The first thing I do after an assembly is always a contig length vs. coverage plot to estimate the repeat content. It's usually quite easy to see the repeats.

rgds
Mads
Forum: Bioinformatics 12-22-2011, 11:32 PM
Replies: 5
Views: 2,017
Posted By MadsAlbertsen
We've done anything from 200x-2000x (depending on...

We've done anything from 200x-2000x (depending on if we can fill the machine..) and I do not see much difference in the assembly above 300x.

We do not use matepairs normally as we are rarely...
Forum: Bioinformatics 12-22-2011, 01:43 AM
Replies: 5
Views: 2,017
Posted By MadsAlbertsen
I would do PE 2x100 and a Matepair of 5Kb. ...

I would do PE 2x100 and a Matepair of 5Kb.

In my experience it is atleast as good if not better than 454 (only done 1x454 genome..).

rgds
Mads Albertsen
Forum: Bioinformatics 06-03-2011, 11:38 AM
Replies: 7
Views: 1,784
Posted By MadsAlbertsen
I would go with a small/medium sized cluster and...

I would go with a small/medium sized cluster and then go for large jobs in the cloud instead.

From my point of view it is way too expensive to scale the computer needs after the peak requirements...
Forum: Bioinformatics 05-26-2011, 11:01 AM
Replies: 9
Views: 2,168
Posted By MadsAlbertsen
I would not try to assemble the data at all. 200k...

I would not try to assemble the data at all. 200k 454 reads seems very low to get any decent assembly even in very simple communities (or even in single genomes).

200.000 reads x 250 bp read...
Forum: De novo discovery 05-02-2011, 08:10 AM
Replies: 8
Views: 2,687
Posted By MadsAlbertsen
I've been doing this to manually close gaps that...

I've been doing this to manually close gaps that can't be assembled using various short read assemblers and it generally works great if you restrict the new denovo assembly to the regions where you...
Forum: RNA Sequencing 04-15-2011, 05:32 AM
Replies: 3
Views: 1,511
Posted By MadsAlbertsen
There are basically two possible problems: ...

There are basically two possible problems:

1) The removal efficiency is highly dependant on intact rRNA. Make sure that rRNA is not degraded before applying MICROBExpress.

Working faster and...
Forum: Bioinformatics 10-23-2010, 01:38 AM
Replies: 7
Views: 2,625
Posted By MadsAlbertsen
Have you considered using the USEARCH package...

Have you considered using the USEARCH package instead of BLAST? It might make it possible to do large scale database search?

rgds
MA
Forum: Bioinformatics 10-20-2010, 10:13 PM
Replies: 7
Views: 2,625
Posted By MadsAlbertsen
You should check: A human gut microbial gene...

You should check: A human gut microbial gene catalogue established by metagenomic sequencing. (doi:10.1038/nature08821)

To my knowledge this is the only study who have published large scale...
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