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zavolanlab/PAQR_KAPAC
Missing conda packages break creation of py2_paqr environment.

Hi there, Python 2.7.11 does not seem to be available to install via the conda install python=2.7.11 step in the py2-paqr virtual environment creation. Additionally, pymongo 3.4.0 does not seem to be ...
  • ClarinetK622
  • 2
  • Opened 
    on Oct 23, 2020
  • #20

zavolanlab/PAQR_KAPAC
Errors when running PAQR step2

Hi, Thanks for developing PAQR_KAPAC. I am facing a problem when running step2 of PAQR with the source code (error shown in the attached figure). Does anyone have idea from which the error comes? Many ...
  • Sylarair
  • 14
  • Opened 
    on Sep 5, 2020
  • #19

zavolanlab/PAQR_KAPAC
Intronic polyadenylation quantification

Hello, First of all: thank you very much for sharing this code with very clear description here! After running the PAQR pipeline successfully, I am getting a list of differential usage of polyA sites ...
  • vvdnoord
  • 2
  • Opened 
    on Mar 19, 2020
  • #17

zavolanlab/PAQR_KAPAC
Updating mm10 annotation files with PolyASite 2.0 release

Thanks for providing the mm10 annotation files for the poly(A) sites and for the clearly written documentation, I ve been able to get PAQR running on our data pretty smoothly. Judging from the commit ...
  • SamBryce-Smith
  • 6
  • Opened 
    on Jan 7, 2020
  • #15

zavolanlab/PAQR_KAPAC
Further question about how to properly set up the sample relationships

A bit confused about the appropiate way to set up the samples in the config.yaml Currently the config.yaml as provided when you download looks likes this: #------------------------------------------------------------------------------- ...
  • aleighbrown
  • 3
  • Opened 
    on Nov 27, 2019
  • #14

zavolanlab/PAQR_KAPAC
config.yaml has a readlength parameters which is not mentioned in the README

In the config.yaml there s a parameter for readlength which I did not see mention of in the readme and only just noticed; line 99. # read length of the study (when different samples have different read ...
  • aleighbrown
  • 1
  • Opened 
    on Nov 27, 2019
  • #13

zavolanlab/PAQR_KAPAC
Infer relative usage: IndexError: list index out of range

Hi, I am running the example data through the snakemake pipeline to test it. Part one proceeds successfully, however I get a list index out of range error while it runs the deNovo-used-sites-and-usage-inference.single_distal_included.py ...
  • peterkilfeather
  • 2
  • Opened 
    on Nov 21, 2019
  • #12

zavolanlab/PAQR_KAPAC
Error in rule infer_relative_usage: TypeError: not all arguments converted during string formatting

Hello, There is no problem in part_one, and all samples are in no_bias_samples.out. But there is a problem in infer_relative_usage of part_two: TypeError: not all arguments converted during string formatting ...
  • yangjywhu
  • 1
  • Opened 
    on Nov 20, 2019
  • #11

zavolanlab/PAQR_KAPAC
annotation files for hg19

Hello! We have annotation files of hg38 and mm10. But I need to run PAQR in our data, which has been mapped to hg19. Could you provide the annotation files of hg19? or, can I change the coordinate from ...
  • yangjywhu
  • 1
  • Opened 
    on Nov 14, 2019
  • #10

zavolanlab/PAQR_KAPAC
Error in rule infer_relative_usage UnboundLocalError: local variable 'end_idx' referenced before assignment

############## Started script on 12-11-2019 at 11:39:43 ############## [INFO] Tue Nov 12 11:40:52 2019 Finished reading input [INFO] Distal site skipped due to conflicting global break points in all samples ...
  • aleighbrown
  • 4
  • Opened 
    on Nov 12, 2019
  • #9
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