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Forum: Bioinformatics 01-27-2014, 12:34 AM
Replies: 2
Views: 1,488
Posted By RickBioinf
Question Transcriptomics analysis

Hi all,

I am a newbie in the field of transcriptomics analysis and I want to get more familiar with it. I know I should first normalize (or should there also be a transformation step) the results...
Forum: Bioinformatics 12-18-2013, 07:10 AM
Replies: 11
Views: 2,683
Posted By RickBioinf
Oops, forget it. It is already installed on...

Oops, forget it. It is already installed on Bio-linux.

Thanks again!
Forum: Bioinformatics 12-18-2013, 07:07 AM
Replies: 11
Views: 2,683
Posted By RickBioinf
Thanks for the info GenoMax, but unfortunately...

Thanks for the info GenoMax, but unfortunately the link on the website, to download the tool, does not work. Do you have an idea if I can download it in another way?

Cheers
Forum: Bioinformatics 12-18-2013, 06:44 AM
Replies: 11
Views: 2,683
Posted By RickBioinf
Smile Local pattern searching algorithm

Hi everyone,

Does anybody maybe know of a good DNA and/or protein pattern searching algorithm that you can on your local server? I've been looking up a couple of them on the web, but they are all...
Forum: Bioinformatics 09-23-2013, 01:17 AM
Replies: 6
Views: 2,366
Posted By RickBioinf
maybe I'm mistaken, but isn't this just a SAM...

maybe I'm mistaken, but isn't this just a SAM file?
Forum: Bioinformatics 09-16-2013, 04:45 AM
Replies: 6
Views: 2,846
Posted By RickBioinf
I think he means that you first find the 'GG' and...

I think he means that you first find the 'GG' and then take the 20 bases before the 'GG' and the 'GG' itself, so not splitting the sequences in 22-mers before hand.
Forum: Bioinformatics 09-13-2013, 12:26 AM
Replies: 5
Views: 4,243
Posted By RickBioinf
When I was working with this I found out that the...

When I was working with this I found out that the "synonyms file" is not always quite up-to-date with the Silva database. What you could do is update it yourself or ask the MEGAN guy to do this for...
Forum: Bioinformatics 09-06-2013, 01:16 AM
Replies: 3
Views: 2,002
Posted By RickBioinf
Search for an alignment tool. There are multiple...

Search for an alignment tool. There are multiple alignment tools out there, e.g. BLAST, BWA, Bowtie. BLAST is the most sensitive, but takes the longest. You should therefore look what best suits your...
Forum: Bioinformatics 07-24-2013, 12:55 AM
Replies: 5
Views: 1,644
Posted By RickBioinf
With 16S I'd recommend firstly looking at an...

With 16S I'd recommend firstly looking at an alignment tool, the alignment tool can be the hardest one to figure out. There are alot and they all have their benefits.

QIIME has (close to) all the...
Forum: Bioinformatics 07-24-2013, 12:31 AM
Replies: 5
Views: 1,644
Posted By RickBioinf
Depends on what kind of metagenomics you are...

Depends on what kind of metagenomics you are carrying out, whole genome or 16S?
Forum: Bioinformatics 06-26-2013, 04:45 AM
Replies: 8
Views: 1,915
Posted By RickBioinf
I prefer to make my own pipeline workflow, so I...

I prefer to make my own pipeline workflow, so I know exactly what the code is and I can change everything. But when it's really necessary I like to use Galaxy.
Forum: Bioinformatics 06-26-2013, 04:01 AM
Replies: 2
Views: 1,179
Posted By RickBioinf
ps. any input is welcome

ps. any input is welcome
Forum: Bioinformatics 06-26-2013, 02:32 AM
Replies: 2
Views: 1,179
Posted By RickBioinf
InDel finding tool

I'm making an InDel finding tool for NGS data and would like to know from the community what do you think would be the best features to include in this? And is it maybe better to make a biologist...
Forum: Metagenomics 02-08-2013, 02:41 AM
Replies: 10
Views: 5,795
Posted By RickBioinf
there are too many variables to answer your...

there are too many variables to answer your question can you be more specific?
Forum: Metagenomics 01-13-2013, 11:57 PM
Replies: 3
Views: 2,524
Posted By RickBioinf
I know that wikipedia is not the most reliable...

I know that wikipedia is not the most reliable site in the world, but for this it is correct. So if you ever want to know what everything is: http://en.wikipedia.org/wiki/Nucleic_acid_sequence
Forum: Metagenomics 01-08-2013, 04:18 AM
Replies: 3
Views: 1,263
Posted By RickBioinf
Hi FGP, Just wanted to let you know there is...

Hi FGP,

Just wanted to let you know there is an update for the Illumina HiSeq that will let you be able to get 150bp reads, might be handy.

Rick
Forum: Metagenomics 01-08-2013, 12:22 AM
Replies: 3
Views: 1,263
Posted By RickBioinf
Hi FGP, You want to use an Illumina HiSeq...

Hi FGP,

You want to use an Illumina HiSeq for this? Or something else? If you use the HiSeq I would say go for the V4 region, this is the best region to use if you are going for just one region....
Forum: Bioinformatics 12-24-2012, 05:03 AM
Replies: 0
Views: 1,030
Posted By RickBioinf
How to get the highest accuracy with BWA for metagenomics

I am trying to use BWA for my metagenomics project, but I can't really find what parameters I should use for this.
Does anyone here maybe know this?
Forum: Bioinformatics 12-20-2012, 12:19 AM
Replies: 2
Views: 3,012
Posted By RickBioinf
Hi OllyBolly, I am doing this right now and...

Hi OllyBolly,

I am doing this right now and am using multiple different databases (RDP, Silva and Greengenes).
If you look at: MEGAN-download...
Forum: Bioinformatics 12-17-2012, 01:38 AM
Replies: 10
Views: 2,368
Posted By RickBioinf
Maybe try and right a Perl file, I think that...

Maybe try and right a Perl file, I think that would be your best option for this.
I personally don't know a tool for this.
Forum: Bioinformatics 11-30-2012, 12:40 AM
Replies: 14
Views: 6,394
Posted By RickBioinf
For more respondents maybe also try:...

For more respondents maybe also try: http://www.reddit.com/r/bioinformatics
Forum: Metagenomics 11-29-2012, 11:44 PM
Replies: 3
Views: 3,789
Posted By RickBioinf
Hi cliffbeal, Thank you for replying. I...

Hi cliffbeal,

Thank you for replying.
I see that I haven't been complete. I'm talking about the V4 region in the 16S.
With mismatch ratio (maybe I'm using the wrong term here) I mean that when...
Forum: Metagenomics 11-28-2012, 06:02 AM
Replies: 3
Views: 3,789
Posted By RickBioinf
Exclamation Removing Chimeric sequences from Metagenomics samples

I'm making 2 Metagenomics pipelines (one for WGS and one for 16S) and I just found out about Chimeras and I think I understand what they are.

Chimeric sequences are products when 2 halves of a PCR...
Forum: Bioinformatics 11-27-2012, 01:37 AM
Replies: 3
Views: 1,436
Posted By RickBioinf
I think you have by now found what you were...

I think you have by now found what you were looking for, but here are a couple of good tools for WGS:
- MetaVelvet, MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from...
Forum: Bioinformatics 11-27-2012, 01:16 AM
Replies: 13
Views: 2,486
Posted By RickBioinf
I would say for the visualisation of alignment...

I would say for the visualisation of alignment tools, such as BLAST, RDP classifier and RAPSearch, you could use MEGAN. It gives back good looking clado/phylograms and can also look in the KEGG/SEED...
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