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vallotlab / scChIPseq

Analysis of single-cell ChIP-seq datasets : From count matrices to differential analysis
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Where are the bam files? #1

Closed millerh1 closed 5 years ago

millerh1 commented 5 years ago

Hello!

I am unable to locate the BAM files for the ChIP-Seq experiments. It says in the README:

"To run the analysis for the 4 datasets in the paper first download all the matrices and bam files in the repo root."

These files do not seem to be included in the GEO entry or mentioned anywhere in the article. Where can the bam files be downloaded from? I am really hoping to avoid re-analyzing the fastq files if possible!

I saw that you may download the 10X bam files for the scRNA-Seq but I don't see any option to do so for the scChIP-Seq experiment.

Thank you!

gamazeps commented 5 years ago

Hi Henry !

The bam files are only needed if you want to do peak calling, which may not bee what you are looking for. Launching the command without the b1 or b2 arguments should work fine, so you can analyse the data without them (at least for now).

We are looking into why they are not in the GEO.

Cheers

gamazeps commented 5 years ago

Hi again Henry !

The bams can be found on this figshare

Cheers, Felix

millerh1 commented 5 years ago

Thank you so much for the response!!

That worked for me and I was able to successfully run the code in your repository. I was just wondering if you happened to have an mm10 alignment file for the HBCx-22 and HBCx-22 TamR samples as well? I noticed that it wasn't in the run_paper.sh commands and wasn't in figshare, but that there were in count tables in GEO for those samples (e.g. GSM3290892 supplementary files). Thank you again for looking into this!

Pacomito commented 5 years ago

Hi Henry, Great to know it worked for you! We put the matrices on GEO for HBCx_22 mm10 but don't analyze it in the paper as there are very few cell count therefore we didn't upload the bam files. Best, Pacôme

millerh1 commented 5 years ago

Understood! Thank you again for looking into this!

Best, Henry Miller