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Old 09-23-2015, 01:48 AM   #1
Location: Vilnius

Join Date: Apr 2012
Posts: 11
Default MiSeq data analysis using Galaxy

Hi all,

I'm considering to analyse MiSeq resequencing FASTQ data (pair-end, adapter free) using Galaxy tools. Just to be sure my workflow-thinking is correct could you check these steps:
1. "Filter by quality" uploaded fastq files to remove poor quality reads (e.g. filter setting >Q30)
2. Map (align) to h19 using "BWA for Illumina" (or Bowtie2?)
3. "MarkDuplicates" in BAM using picard.
4. Annotate using "ANNOVAR Annotate VCF"

is that correct?
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