Question: Checking coverage of yeast whole genome sequencing data
0
gravatar for skhan
3 months ago by
skhan40
skhan40 wrote:

I have WGS data (2x150b paired end NextSeq reads) for Yeast (sacCer3) and would like to know how much coverage the data has relative to the reference genome.

My plan here is to use STAR to align the dataset to the reference (sacCer3), and then Qualimap to analyze the resultant BAM file.

Is STAR the right alignment tool to use for yeast WGS data? Or is STAR better suited to RNA-Seq data ... and so I should be using a tool like BWA-Mem?

Does the choice of tool matter if the dataset was from mouse, rat, or human as opposed to yeast?

Thanks,

skhan

star alignment yeast • 105 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by skhan40
2
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

For DNA sequences, BWA MEM is a better tool choice. Mapping against Yeast will work fine.

Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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