Make ATAC fragment files public?

[plger]

Hi,
thanks for this great resource!
It's especially nice that you provide the peaks here given that the raw data is under restricted access and it's quite a pain to get it (I've been waiting for a month). I was wondering whether it would be possible to also make available somewhere the ATAC-seq fragment files (i.e. start and end coordinates of fragments) of the sorted populations (e.g. FP NeuN+, etc.). Contrarily to the bam files this would not contain any potentially identifying information, and would enable a much broader range of the scientific community to re-use the data.
Thanks in advance,
Pierre-Luc

[aanderson54]

Hi,
Thanks for reaching out about data availability! We want to make sure that our data can easily be used by the community. We did not generate ATAC-seq fragment files as part of our data processing, but I have added the ATAC-seq peaks to the GitHub page. Are the peaks sufficient for your use? If not, we can work on generating those files as well.

Ashlyn

[plger]

Hi Ashlyn,
Thanks a lot for the answer! I'm afraid the peaks are not sufficient for my purposes, but I'm sure it's going to be of use to someone!
One way of generating fragment files is using bedtools's bamToBed and doing some light filtering, e.g. assuming that the bam files are sorted by QNAME, something like:

samtools view -b -f 3 -F 1804 file.bam | bamToBed -bedpe -i /dev/stdin | cut -f 1,2,6,9 | sortBed -i - | gzip -c > frags.tsv.gz

If there's a way you could share this, it would be a big help!
(And congrats on the nice paper, it's an extremely useful resource given the paucity of TF binding data in the brain!)
Pierre-Luc

[plger]

Dear Ashlyn,
I'm sorry to bug you again with this, but as our NRGR access request is still pending after 3 months, if there is a possibility you could make the fragment files available, it would be a tremendous help for us, and most likely for others as well.
Cheers,
Pierre-Luc