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Forum: General 01-10-2013, 08:07 AM
Replies: 0
Views: 891
Posted By nullalleles
tBLASTx cDNA in genomic DNA assembly

I have been using the NCBI's BLAST stand-alone program to interrogate in-house transcriptome assemblies of different insect species. Using tBLASTx, I can often find matches between a given gene from...
Forum: RNA Sequencing 09-24-2012, 10:21 AM
Replies: 9
Views: 10,727
Posted By nullalleles
Question paired-end vs. single end for differential expression analysis

There are a variety of posts suggesting either single-end or paired-end mRNA-sequencing is better for differential expression analysis. I have noticed many people defaulting to paired-end reads,...
Forum: Bioinformatics 09-06-2011, 11:46 AM
Replies: 15
Views: 5,485
Posted By nullalleles
Does anyone know if SomaticSniper can be used...

Does anyone know if SomaticSniper can be used with a Unix system?
Forum: Genomic Resequencing 07-18-2011, 07:28 AM
Replies: 1
Views: 3,620
Posted By nullalleles

The above code should have contained the argument "-L" for the interval list (bed) file and also a "-R" for the reference fasta file!
Forum: Genomic Resequencing 07-12-2011, 12:22 PM
Replies: 1
Views: 3,620
Posted By nullalleles
GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment

I am trying (and failing) to call SNPs using a reference file (.BED) specifically for the Agilent 50Mb Sureselect enrichment sequencing. I am using the GATK UnifiedGenotyper with the following...
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