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vanheeringen-lab / seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
https://vanheeringen-lab.github.io/seq2science
MIT License
156 stars 26 forks source link

FR: scATAC test samples #366

Closed siebrenf closed 1 year ago

siebrenf commented 4 years ago

@JGASmits, could you provide a (set of) minimal sample(s) that can be used for testing?

Maarten-vd-Sande commented 4 years ago

I think I will write a script to generate those files for ATAC-seq anyways, so I could do it for scATAC & ChIP as well

JGASmits commented 4 years ago

My smallest files that can still generate a SNAPobject still take like 5 min to run succesfully

Maarten-vd-Sande commented 4 years ago

I am thinking about just making a really really small fastq and only keep 1 chromosome instead of full genome. Should speed things up considerably

siebrenf commented 4 years ago

if it works for rna-seq too we can throw out the old batch. they are too similar for differential gene expression anyway