d-gebert / Fly_piC_evo_del

Code and annotation repository accompanying the Paper "Large Drosophila Germline piRNA Clusters are Evolutionarily Labile and Dispensable for Transposon Regulation" (Gebert et al. 2021, https://doi.org/10.1016/j.molcel.2021.07.011)
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How to create final pic.bed files? #1

Open Jung19911124 opened 1 year ago

Jung19911124 commented 1 year ago

Hi, I have read your paper "Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation" and am very impressed. I would like to try to see if a similar trend can be observed using my unpublished data of some species of lepidoptera.

I have one question. Your *pics.bed file contains more information than the gtf file output by ProTRAC. Could you tell me how you obtained the data from columns 13 to 30, i.e. from "pp_zscore" to "RC"? Thanks in advance.

Sincerely, Jung

d-gebert commented 1 year ago

Hi Jung, sounds interesting!

For the extended bed file I’ve written a Perl script as a wrapper for proTRAC, which adds z-scores and other stuff. I’ll try to add the updated thing soon, but what I’ve already done right now is uploading the basic wrapper script with the proTRAC and pingpong scripts as well.

Hope that’s useful, but I’ll let you know once the updated wrapper is online.

All the best Daniel

On 19. May 2023, at 10:15, Jung19911124 @.***> wrote:

Hi, I have read your paper "Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation" and am very impressed. I would like to try to see if a similar trend can be observed using my unpublished data of some species of lepidoptera.

I have one question. Your *pics.bed file contains more information than the gtf file output by ProTRAC. Could you tell me how you obtained the data from columns 13 to 30, i.e. from "pp_zscore" to "RC"? Thanks in advance.

Sincerely, Jung

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Jung19911124 commented 1 year ago

Hi Daniel,

ProTRAC_wrapper.pl you kindly uploaded worked well on my dataset so far! I am looking forward to obtaining the complete *final.piC.bed files and finding different piC properties between Diptera and Lepidoptera. Thanks!

Sincerely, Jung