ddaneels, for clipping the 3' end I use Sickle (https://github.com/najoshi/sickle). It is generally used for read trimming, as reads tend to have a low quality on the 3' end and the 5' end, so this tool allows trimming based on the quality from the fastq file.
Regarding the reference file, I usually use a single FASTA file as the reference which includes all chromosomes, instead of per chromosome. It takes more time to map for the entire genome, but unless you want to study a specific region of your read data, it makes more sense to use the complete reference as an exploratory analysis.
Regarding the reference file, I usually use a single FASTA file as the reference which includes all chromosomes, instead of per chromosome. It takes more time to map for the entire genome, but unless you want to study a specific region of your read data, it makes more sense to use the complete reference as an exploratory analysis.
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