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Search: Posts Made By: Dameon
Forum: Bioinformatics 10-02-2015, 05:08 PM
Replies: 3
Views: 1,471
Posted By Dameon
Awesome. Thank you for looking into this for us.

Awesome. Thank you for looking into this for us.
Forum: Bioinformatics 09-22-2015, 10:58 AM
Replies: 3
Views: 1,471
Posted By Dameon
I get the same error. The paths/urls must have...

I get the same error. The paths/urls must have changed on the Kegg repository backend. It looks like the error might be coming from the keggLink function call from within kegg.gsets.
Forum: Bioinformatics 03-22-2012, 09:41 AM
Replies: 2
Views: 2,077
Posted By Dameon
From what I can tell, you are filtering on a...

From what I can tell, you are filtering on a maximum depth of 1000. Try using a minimum depth of 5 ad allowing SNP calls from Anomalous reads. I also found turning BAQ off helps with sensitivity as...
Forum: Bioinformatics 03-21-2012, 01:08 PM
Replies: 7
Views: 4,398
Posted By Dameon
Try using snpEff. If you have a...

Try using snpEff. If you have a reference_genome.fasta and either a .gff or .gtf file of the CDS regions, you can build your own custom database for SNP effect prediction. In the case of bovine, if...
Forum: Bioinformatics 02-22-2012, 07:46 AM
Replies: 30
Views: 11,820
Posted By Dameon
I recommend MapSplice for detecting gene fusions...

I recommend MapSplice for detecting gene fusions in PE data. I use the full-running, cluster, MapPer, and filter-fusion-by-repeat options. I like how it reports putative gene fusions in an easily...
Forum: Bioinformatics 02-01-2012, 12:59 PM
Replies: 6
Views: 4,874
Posted By Dameon
No problem. I was just incorporating that little...

No problem. I was just incorporating that little bit into one of my perl scripts yesterday. Glad it could help.
Forum: Bioinformatics 02-01-2012, 12:57 PM
Replies: 1
Views: 1,736
Posted By Dameon
snpEff will identify synonymous and...

snpEff will identify synonymous and non-synonymous mutations for SNP data in pileup format. I am not sure how it will perform with population data though.
Forum: Bioinformatics 02-01-2012, 12:36 PM
Replies: 6
Views: 4,874
Posted By Dameon
samtools faidx /path/to/your/genome.fa...

samtools faidx /path/to/your/genome.fa chr1:base_position
Forum: Bioinformatics 12-21-2011, 06:56 AM
Replies: 3
Views: 1,768
Posted By Dameon
I believe that Cuffdiff uses LocFit Regression in...

I believe that Cuffdiff uses LocFit Regression in the case were there are no biological replicates to estimate dispersion with inferences made from a Poisson distribution. I do not believe that...
Forum: Bioinformatics 12-20-2011, 06:59 AM
Replies: 27
Views: 11,585
Posted By Dameon
Create a bed file of your Agilent SureSelect...

Create a bed file of your Agilent SureSelect targets and use BEDtools to merge adjacent targets and then slopBed to add 50 bps to either side of your merged targets. Then use Bedtools BedtoBam to...
Forum: Bioinformatics 12-20-2011, 06:50 AM
Replies: 2
Views: 5,427
Posted By Dameon
For many of the VCFtools, you also need to bgzip...

For many of the VCFtools, you also need to bgzip and tabix index VCf files. And Laura is correct, your installation of VCFtools should be in your $PATH env variable as well as exported to your...
Forum: Bioinformatics 12-19-2011, 07:01 AM
Replies: 2
Views: 1,900
Posted By Dameon
I would use GATK available from the Broad's...

I would use GATK available from the Broad's Genome Analysis Toolkit and indel realign, recalibrate, and call and filter genotypes following the Broad's recommended best practices. Then I would take...
Forum: Bioinformatics 12-12-2011, 09:29 AM
Replies: 12
Views: 8,435
Posted By Dameon
The only problems I forsee of using GATK to call...

The only problems I forsee of using GATK to call variants from RNA-seq data is the filtering. You want to set the Unified Genotyper as sensitive as possible, don't worry about this as GATK is very...
Forum: Bioinformatics 12-12-2011, 07:30 AM
Replies: 12
Views: 8,435
Posted By Dameon
I use GATK to call variants from TopHat aligned...

I use GATK to call variants from TopHat aligned BAM files. First, you'll need to add @RG information and sort using PICARD tools so as to configure the BAM files for GATK; otherwise, it will fail. ...
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