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Search: Posts Made By: Hobbe
Forum: Bioinformatics 08-15-2013, 03:05 AM
Replies: 4
Views: 2,576
Posted By Hobbe
No, you are right. That was my mistake. However,...

No, you are right. That was my mistake. However, I can't say I really like the output of that one, so I'd really like to get more suggestions that give more clear "easy on the eye" output.
Forum: Bioinformatics 08-15-2013, 01:49 AM
Replies: 4
Views: 2,576
Posted By Hobbe
Graphical representation of gene level synteny between genomic regions

So, I have a de novo sequenced genome that has a section deleted when compared to a closely related species. Basically, around the deleted region, synteny is strongly preserved with orthologous genes...
Forum: RNA Sequencing 10-23-2012, 01:15 AM
Replies: 2
Views: 2,167
Posted By Hobbe
The names are taken from your genome fasta file,...

The names are taken from your genome fasta file, not the reference gff file. This is of course logical, since the junctions are results from your mapping of reads to the genome. Seems tophat finds...
Forum: Bioinformatics 10-18-2012, 01:01 AM
Replies: 5
Views: 3,297
Posted By Hobbe
In addition to Newbler, where I would probably go...

In addition to Newbler, where I would probably go the de novo route, I can recommend MIRA. You might need to down-sample a bit, but MIRA should do a really good job. The only reason that I am not...
Forum: De novo discovery 06-12-2012, 05:40 AM
Replies: 9
Views: 4,106
Posted By Hobbe
Blast2GO is great. I think you will be very happy...

Blast2GO is great. I think you will be very happy with the results.
Forum: Bioinformatics 05-23-2012, 12:57 AM
Replies: 5
Views: 7,905
Posted By Hobbe
The bed file seems very sparse to me. BedToBam...

The bed file seems very sparse to me. BedToBam seems to be looking for a name which should be in a fourth column. Haven't really tried BedToBam, but that is my guess.
Forum: Bioinformatics 03-20-2012, 05:01 AM
Replies: 252
Views: 106,495
Posted By Hobbe
I am having problems using SSPACE basic with my...

I am having problems using SSPACE basic with my 454 paired-end data, and was hoping to get some help here. SSPACE runs fine using my Illumina PE data, but my 454-data has much longer insert-sizes...
Forum: Bioinformatics 03-13-2012, 02:41 AM
Replies: 12
Views: 4,529
Posted By Hobbe
Go here ...

Go here
http://seqanswers.com/forums/forumdisplay.php?f=18

An then click on New Thread to the left.
Forum: Bioinformatics 03-13-2012, 02:33 AM
Replies: 12
Views: 4,529
Posted By Hobbe
Start a new thread please, with this same...

Start a new thread please, with this same question. But to get you started, check out Scripture at http://www.broadinstitute.org/software/scripture/home
Forum: Bioinformatics 03-05-2012, 06:01 AM
Replies: 6
Views: 3,041
Posted By Hobbe
Shrimp2 is easy to use and runs very well on...

Shrimp2 is easy to use and runs very well on several cores if you have them, so it is fairly quick. In my experience, it maps well too.
Forum: Bioinformatics 02-27-2012, 05:50 AM
Replies: 29
Views: 11,900
Posted By Hobbe
The trimmer Trimmomatic outputs files with intact...

The trimmer Trimmomatic outputs files with intact pairs as well as files with single reads. It should be able to split your files in the way you want, as well as do trimming at the same time if you...
Forum: Bioinformatics 02-09-2012, 12:31 AM
Replies: 1
Views: 1,062
Posted By Hobbe
How to identify incorrectly fused gene models

When annotating a eukaryotic genome de novo, I find it tricky to identify gene models that in reality are two genes that are incorrectly fused. Rather than correctly identifying the stop codon, the...
Forum: Bioinformatics 01-11-2012, 06:34 AM
Replies: 12
Views: 3,249
Posted By Hobbe
bbsinfo, there are (as far as I know) three ways...

bbsinfo, there are (as far as I know) three ways to find introns.

1) You could do a spliced alignment of some kind of assembled transcripts/ESTs using for example Blat (if you are working in...
Forum: Bioinformatics 11-22-2011, 05:36 AM
Replies: 2
Views: 3,325
Posted By Hobbe
Gene prediction has a random part to it, so even...

Gene prediction has a random part to it, so even if you run the same program twice with exactly the same parameters, you would probably get a different amount of genes. If you try different training...
Forum: Bioinformatics 11-04-2011, 05:32 AM
Replies: 1
Views: 2,229
Posted By Hobbe
Tophat junction coordinates

I am using Tophat on some Solid fungal transcriptomes and want to use the junctions found by Tophat as intron hints in the Augustus gene finder. In the junctions.bed file produced, the coordinates...
Forum: Bioinformatics 09-23-2011, 07:00 AM
Replies: 12
Views: 4,184
Posted By Hobbe
Repeatmasker both identifies and masks...

Repeatmasker both identifies and masks repeat-elements. Some assembly programs, like Mira, also mark repeat regions with tags. In Mira you can check the sequences identified as repeats in the...
Forum: Bioinformatics 09-05-2011, 01:21 AM
Replies: 11
Views: 31,521
Posted By Hobbe
Did you check out Blast2go.org? I find it to be...

Did you check out Blast2go.org? I find it to be an excellent and very user friendly option for doing these kinds of annotations.
Forum: SOLiD 08-15-2011, 11:46 PM
Replies: 6
Views: 5,342
Posted By Hobbe
Blat is the preferred program to use for spliced...

Blat is the preferred program to use for spliced mapping (see the Augustus Rnaseq instructions). You really need those intron hints to get correct gene models. Blat doesn't work on Solid data though....
Forum: SOLiD 05-13-2011, 07:15 AM
Replies: 6
Views: 5,342
Posted By Hobbe
Thanks for the reply. No, we are working in color...

Thanks for the reply. No, we are working in color space. Sequences converted to sequence space would too easily become wrong if there are any errors in the original colorspace reads. However, if you...
Forum: SOLiD 05-09-2011, 12:03 AM
Replies: 6
Views: 5,342
Posted By Hobbe
Splice site prediction with solid rna-seq data

Hi all

We are having problems predicting splice sites from our Solid rna-seq data. We have a draft genome (125Mb, a eukaryote) assembled from 454-data and are now trying to map our Solid reads to...
Forum: Bioinformatics 02-17-2011, 11:38 PM
Replies: 0
Views: 1,623
Posted By Hobbe
How are you comparing assemblies?

I am in a project working with a 120 MB eukaryote genome. We have tried a number of assemblers on our 454 data (Mira, Abyss, different versions of Newbler, Celera, Arachne, and possibly some more,...
Forum: Bioinformatics 11-16-2010, 02:31 AM
Replies: 0
Views: 1,754
Posted By Hobbe
Gene prediction programs that work with multi-fasta files

We have a draft genome of a fungus with around 4000 contigs. I have been using Genemark-ES on the multiple contig fasta file, but it finds genes that stretches over two contigs, and thus do not...
Forum: Bioinformatics 11-16-2010, 02:18 AM
Replies: 13
Views: 6,439
Posted By Hobbe
Try saving (in Artemis) your gene prediction...

Try saving (in Artemis) your gene prediction results in another format such as EMBL or Genbank. I use EMBL. In this format you should be able to add the color information you need.
Forum: Bioinformatics 10-05-2010, 06:41 AM
Replies: 2
Views: 2,388
Posted By Hobbe
Thanks Francois, that is a great suggestion. I am...

Thanks Francois, that is a great suggestion. I am fiddling around with it now, it just might work.

Anyone else have a suggestion?
Cheers,
Henrik
Forum: Bioinformatics 10-05-2010, 01:59 AM
Replies: 2
Views: 2,388
Posted By Hobbe
Genome browser that work well with multiple contig files

I have assembled a fungal genome de novo using Mira which has resulted in a multiple entry fasta file of over 4000 contigs. We have so far found all genes we have been looking for and have no plans...
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