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StevenWingett / FastQ-Screen

Detecting contamination in NGS data and multi-species analysis
https://stevenwingett.github.io/FastQ-Screen/
GNU General Public License v3.0
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pair-end screen #26

Closed jeongmeani closed 4 years ago

jeongmeani commented 4 years ago

Hi,

using fastq-screen, i check contamination of ngs data. but i got pair-end data and fastq-screen does not support this mode.

so how can i handle this? would i merge R1 and R2 to check the sample itself?

Best Regards

Jeongmin

StevenWingett commented 4 years ago

Hi Jeongmin,

Process the R1 and R2 files separately with FastQ Screen.

You are trying to identify contamination and mapping the files separately is a better way to do this. For example, suppose the contamination was more prevalent in, say R1. By mapping separately you would be able to identify this bias.

I hope that helps.

All the best,

Steven