Hi,
I am responsible for developing FastQ Screen.
The standard way to remove contamination is:
Run FastQ Screen (latest version) with --subset (to process the entire dataset) and --nohits. In the config file include the Bowtie1/2 indices of all the potential contaminants (human genome indices should not be included).
A FastQ file should then be produced containing all the reads that did not map to any of the contaminants.
I am wondering, why do you need to only remove the hits that are classified as 'one-hit/one-library' AND 'multiple-hits/one-library'? Also is this single-end data?
Please feel free to contact me directly to discuss this further.
Kindest regards,
Steven W
I am responsible for developing FastQ Screen.
The standard way to remove contamination is:
Run FastQ Screen (latest version) with --subset (to process the entire dataset) and --nohits. In the config file include the Bowtie1/2 indices of all the potential contaminants (human genome indices should not be included).
A FastQ file should then be produced containing all the reads that did not map to any of the contaminants.
I am wondering, why do you need to only remove the hits that are classified as 'one-hit/one-library' AND 'multiple-hits/one-library'? Also is this single-end data?
Please feel free to contact me directly to discuss this further.
Kindest regards,
Steven W
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