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?
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?
