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4.6 years ago
kelwick3
•
0
Hi everyone,
I was given .fastq files from the Ion S5 system of human mitochondrial DNA. I have no idea how to analyze these. I was trying to use galaxy to convert the .fastq to .bam (to use in IGV) but the files wouldn't show up in IGV. I then tried to convert .bam to .csv to see if that would be easier to visualize the data and it was not.
Can anyone give me direction as to best analyze my data? Do I need to map my .fastq to a reference genome first? Do I need to trim the barcodes/adapters? Do I need to filter out the poor quality sequences first? I'm not really sure where to begin and what tools to use to do this.
Any help is appreciated!
You need to map the reads to a ref genome first, you'll get a bam with that process. You can do QC check with FastQC, I don't think you need to trim off adapters but FastQC will show you if it contains adapters (or recurrent sequences).
Best thing is to play yourself with filters or not, it is hard to give advice when we are not familiar with your dataset. Read some tutorials about NGS for DNAseq.