Hi to all,
I've been experiencing some problems trimming the adapters and filtering by quality my paired-end Illumina reads.
As fas as i know if i want to use FASTX-TOOLKIT (included in Galaxy) i have to treat my data as single-end, trim the adapter of the forward reads first and then proceed with the reverse reads. And same thing for the filtering by quality. Right?
Does anyone know if i can combine forward/reverse reads in a unique file with the FASTQ joiner (also included in Galaxy) and then proceed with the trimming of the adapters and the filtering by quality? If i do that, am i going to be able to remove the adapters of both directions reads? Am i going to be able to keep the broken pairs?
I was reading that there is another toolkit, NGS QC TOOLKIT that allows you to work with paired-end reads and keep the broken pairs after the trimming and thinning. Did anyone try it? I think that has no galaxy option...
Thanks,
I've been experiencing some problems trimming the adapters and filtering by quality my paired-end Illumina reads.
As fas as i know if i want to use FASTX-TOOLKIT (included in Galaxy) i have to treat my data as single-end, trim the adapter of the forward reads first and then proceed with the reverse reads. And same thing for the filtering by quality. Right?
Does anyone know if i can combine forward/reverse reads in a unique file with the FASTQ joiner (also included in Galaxy) and then proceed with the trimming of the adapters and the filtering by quality? If i do that, am i going to be able to remove the adapters of both directions reads? Am i going to be able to keep the broken pairs?
I was reading that there is another toolkit, NGS QC TOOLKIT that allows you to work with paired-end reads and keep the broken pairs after the trimming and thinning. Did anyone try it? I think that has no galaxy option...
Thanks,
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