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Search: Posts Made By: jjohnson
Forum: Bioinformatics 01-31-2012, 12:55 PM
Replies: 10
Views: 3,795
Posted By jjohnson
If you are new to NGS analysis, I could also...

If you are new to NGS analysis, I could also recommend using a commercial platform such as CLC or DNANexus for RNA-Seq analysis. CLC is a local workbench with yearly license fees (very reasonable...
Forum: Bioinformatics 01-31-2012, 12:52 PM
Replies: 2
Views: 1,497
Posted By jjohnson
I assume you mean GTF file right? Check out IGV...

I assume you mean GTF file right? Check out IGV from the Broad (http://www.broadinstitute.org/igv/)
Forum: Bioinformatics 01-27-2012, 10:22 AM
Replies: 6
Views: 3,408
Posted By jjohnson
I would bin the valid pairs and singletons (those...

I would bin the valid pairs and singletons (those with mates removed due to quality trimming/filtering) into 2 separate fastq files. Velvet can accept mutiple files and then you can paramertize...
Forum: Sample Prep / Library Generation 01-23-2012, 10:21 AM
Replies: 1
Views: 5,464
Posted By jjohnson
I would start by signing up for webinars through...

I would start by signing up for webinars through Illumina. They cover many of the topics below. You just need to create an account and enter your serial number of your machine to get started. If...
Forum: RNA Sequencing 01-19-2012, 11:15 AM
Replies: 6
Views: 2,569
Posted By jjohnson
I personally like Trans-ABySS which analyzes...

I personally like Trans-ABySS which analyzes ABySS-assembled contigs. But, you can;t go wrong with SW out of the Broad either. It may be best to try both.

But this may depend on the organism and...
Forum: General 01-05-2012, 10:47 AM
Replies: 5
Views: 3,023
Posted By jjohnson
We use several tools to call, classify, assign...

We use several tools to call, classify, assign confidence, and annotate. A good place to start is the GATK (http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit)website. ...
Forum: Bioinformatics 01-05-2012, 10:35 AM
Replies: 1
Views: 1,201
Posted By jjohnson
Hi Georgio, I would check out CLCBio (or...

Hi Georgio,

I would check out CLCBio (or maybe another vendor - but we have used CLCBio for this). They have a great miRNA analysis pipeline. First you need to detect and trim the adapter, then...
Forum: Bioinformatics 01-04-2012, 07:34 AM
Replies: 1
Views: 1,882
Posted By jjohnson
Jonas and Jaydut, We use SOLiD extensively...

Jonas and Jaydut,

We use SOLiD extensively here at EdgeBio and finds that when aligning transcriptome data, even more than genomic data, the alignments really matter. Just aligning with bfast or...
Forum: Bioinformatics 12-11-2010, 07:49 AM
Replies: 13
Views: 5,763
Posted By jjohnson
Asif, This is a decision that is completely...

Asif,

This is a decision that is completely up to what the project dictates. You could try another assembler, like Celera, and see if you fill in gaps or produce a better assembly. If you want...
Forum: Bioinformatics 12-11-2010, 07:47 AM
Replies: 13
Views: 5,763
Posted By jjohnson
You could also try running the Celera assembler,...

You could also try running the Celera assembler, which has a built in scaffolder and supports all of the data types you mention. http://j.mp/h7uX9i

It can have a pretty steep learning curve, but...
Forum: SOLiD 12-11-2010, 07:36 AM
Replies: 5
Views: 5,813
Posted By jjohnson
You actually align to the genome after aligning...

You actually align to the genome after aligning to mirBase. The steps are filter against a know set of tRNA and rRNA and then what isn't filtered align to mirBase. What doesn't match there is...
Forum: SOLiD 08-25-2010, 06:51 AM
Replies: 6
Views: 3,455
Posted By jjohnson
RNA2MAP, which is part of the SOLiD open source...

RNA2MAP, which is part of the SOLiD open source software community is free to use: http://solidsoftwaretools.com/gf/project/rna2map/

CLC is a commercial package, but you can get a 2 week demo:...
Forum: SOLiD 08-22-2010, 08:57 AM
Replies: 6
Views: 3,455
Posted By jjohnson
Hi EADIE, I think it depends on how you...

Hi EADIE,

I think it depends on how you intend on processing the data. Software like bioscope and CLCBio will dynamically trim your data to remove adapters and non-miRNA sequence. They both also...
Forum: Bioinformatics 02-18-2010, 05:14 PM
Replies: 8
Views: 3,687
Posted By jjohnson
Adnan, AMOS is a pretty large suite of...

Adnan,

AMOS is a pretty large suite of tools, what are you trying to do more specifically, maybe I can share some war stories if I know where to start.
Forum: De novo discovery 02-15-2010, 12:39 PM
Replies: 58
Views: 50,920
Posted By jjohnson
Hi Marcel, Does oases support the use of...

Hi Marcel,

Does oases support the use of SOLiD data. Can I run velvetg_de and feed this into oases?

Justin
Forum: Bioinformatics 01-27-2010, 06:17 AM
Replies: 5
Views: 1,923
Posted By jjohnson
Hey Scientifica, welcome to seqanswers and good...

Hey Scientifica, welcome to seqanswers and good luck with your research. I would check out http://seqanswers.com/forums/showthread.php?t=43 which details SW packages for NGS data analysis. Personal...
Forum: Bioinformatics 01-26-2010, 06:44 AM
Replies: 15
Views: 7,732
Posted By jjohnson
It looks like you are trying to generate a...

It looks like you are trying to generate a consensus fasta file from a mapping/alignment, and you are using ace only because it is what is produced by mosaik (mosaik also produces sam/bam, but not...
Forum: Bioinformatics 01-22-2010, 12:35 PM
Replies: 22
Views: 10,123
Posted By jjohnson
What type of data is it? 454 I assume, maybe...

What type of data is it? 454 I assume, maybe Sanger? There are several option out there for WGS - I don't have much experience with CAP3. Newbler or Celera Assembler could prove to be viable...
Forum: 454 Pyrosequencing 01-22-2010, 12:25 PM
Replies: 1
Views: 1,878
Posted By jjohnson
Hi Ha, The mapper application uses a combo...

Hi Ha,

The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants...
Forum: Bioinformatics 01-22-2010, 12:10 PM
Replies: 15
Views: 7,732
Posted By jjohnson
I find the AMOS toolset...

I find the AMOS toolset (http://sourceforge.net/apps/mediawiki/amos/index.php?title=File_conversion_utilities) convenient for converting between many differnt assembly outputs/inputs.

So, in this...
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