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Forum: Bioinformatics 01-20-2012, 07:44 AM
Replies: 42
Views: 16,577
Posted By jtrivino
Hi all In an analysis of transcriptomics...

Hi all

In an analysis of transcriptomics with cufflinks and cuffcompare I want to filter and eliminate noise, so, eliminate the transfrag "suspicious", for this, I think that the "class code"...
Forum: Bioinformatics 05-13-2011, 09:22 AM
Replies: 0
Views: 1,507
Posted By jtrivino
ssaha2 with 454 Junior


I want to align my 454 Junior dataset with ssaha2.My command shell is:

/share/apps/ssaha2_v2.5.3_x86_64/ssaha2 -rtype 454 -output sam -outfile MID2/454Reads.MID2.sam -save hg19...
Forum: Bioinformatics 05-06-2011, 04:28 AM
Replies: 0
Views: 2,285
Posted By jtrivino
SNPs false positive GATK


I have used GATK for SNPs calling in Solid platforms of a sample with a deep coverage. I have realigned and recalibrated as the pipeline of GATK literature. The result is in general good, but...
Forum: Bioinformatics 03-04-2011, 06:07 AM
Replies: 1
Views: 1,450
Posted By jtrivino
Hi I use samtools sort *.bam *_sort.bam ...


I use
samtools sort *.bam *_sort.bam
samtools index sort.bam
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