I want to add paired end support to my chip-seq software*, but to do that I need some paired end data. Do you know of any public PE chip-seq data? If you have some you could share a tiny subset of, that would also be greatly appreciated.
If you know a way to create fake PE bam files I'll accept that too.
Here you go: http://www.ebi.ac.uk/ena/data/view/SRX1485421
http://www.ebi.ac.uk/ena/data/view/SRP062397
Human: http://www.ebi.ac.uk/ena/data/view/SRR1573750
I have tried a few datasets from sra, but they were not PE, despite the labels. I'll look into those, thanks.
The last one looks interesting, but I could not find the input data (using mobile, that might be it).
No guarantee they are something you could use. They are labelled ChIP-seq and are PE :-)
Yeah, those archive data are often terribly badly labeled. Takes ages to download and then you see that they cannot be used/aren't what you expected after all. Will perhaps try making my own, unless anyone has any datasets with both chip and input (only one of those has to be pe).
Score! The last file was input. Thanks! Ps. other answers still appreciated :)
Damn, with hisat2 you can just give the SRA-nb on the command line and it downloads and aligns it for you. Sweet:
hisat2 -x hg38 --sra-acc SRR1573750 -S chip_SRR1573750.sam