What is the reliable source to download pig(Sscrofa) reference genome?
I want to use it for bismark.
Ensembl - https://useast.ensembl.org/Sus_scrofa/Info/Index
From Ensembl , which files i need to download for alignment?
https://ftp.ensembl.org/pub/release-109/fasta/sus_scrofa/ Depending on if you are using genome - primary assembly from DNA folder or transcriptome - cDNA from that folder
I want to run bismark like:
bismark_genome_preparation [options] /path/to/genome/folder
So which file I need to use?
If you are not sure which file you need, are you sure you're equipped to analyse the data it spits out, or that you are even doing the correct thing for your question?
Try every file. Or read bismark documentation until you're sure which one you need. I'd recommend the latter approach because it takes less effort and yields more knowledge.
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