ToDo List

[HendrikSchultheis]

Keep our new guidelines in mind while working on this!

Please add the respecting issue/ pull request if already in progress. (E.g. '#3')

General

• renaming of ambiguous functions, scripts, etc.
  • reduce_bed.R -> reduce_sequence.R Cluster #17
• set organism as required parameter without default value Motif estiamtion #12
• accept/generate/ keep header in bed files (header starts with #)
  • clustering Cluster #17
  • bed_to_fasta Motif estiamtion #12
• gtf-file as parameter to skip process create_gtf Motif estiamtion #12
• Imporve motif clustering runtime Improving motif clustering #16
• sub_folder for each tool in /bin sorting scripts depending on their function #28
• The BED-format has changed. Check if your script are still working:
  • 1.2
  • 2.1
  • 2.2
• Statistics of your output:
  • 1.1
  • 1.2
  • 2.1 Cluster #43
  • 2.2 2.2 creates json file containing motif sequences #47
  • 3.2??

Bugs

• in the footprints_extraction.py: the output .bed file should include the "strand" column containing only . Peak calling #15
• in the footprints_extraction.py: the output .bed file the last column containing the "bonus_info" should be separated with other separator than TAB Peak calling #15
• in bed_to_fasta.R: Get column nucleotide_sequence and cluster_id as second last and last column, not with fixed indices. ' bed_to_fasta.R: Get column nucleotide_sequence and cluster_id as second last and last column #11'
• get_best_motif.py: Should convert the files to the real MEME-format + removing last header of MOTIF Motif estiamtion #12
• critical wrong names are introduced through motif_filtering step 'updated script. Now the path of subscripts is automatically aquired. … #33'
• column containing 'control_xy' appearing at some point (seems to be motif_filtering correlated) 'updated script. Now the path of subscripts is automatically aquired. … #33'
• Gtf is sometimes not correct formatted 'GTF-formatting issue #18'

Peer Review

• RegGTFExtractor.py (@anastasiia )
• bed_to_fasta.R (by @HendrikSchultheis )
• cdhit_wrapper.R Review cdhit_wrapper.R and reduce_sequence.R #25 (by @renewiegandt )
• footprint_extraction.py Review footprint_extraction v0.1 #22 (by @renewiegandt )
• get_best_motif.py (@JannikHamp )
• compareBed_runinfo.R (@anastasiia @SebastianBeyvers )
• merge_similar_cluster.R (@HendrikSchultheis )
• reduce_sequence.R Review cdhit_wrapper.R and reduce_sequence.R #25 (@renewiegandt )

Wiki

• demo run
• After everything else is done check and update the wiki and README one last time

[HendrikSchultheis]

Alright everyone our first iteration of what we need to do. Please add all missing tasks so we have a comrehensive overview at all times.

[afust]

Hi, some small things I recognized:

• update env file (why is there snakemake?) Motif estiamtion #12
• update README (installation: all dependencies handled by conda env, or do I need to install them before on my own?) Motif estiamtion #12
• check for typos and commands, e.g. conda env create --file hat kein "="! Motif estiamtion #12

[anastasiia]

Here is the presentation. I think it is better, if we are working together this time from the beginning on.

presentation

[anastasiia]

has someone worked with the presentation already and have deleted some slides from my part?

[anastasiia]

someone has also changed the date from 14.01.2019 to 17.12.2018!

and one more question: we write the presentation in german or in english? The last time it was in english, but I see someone writing in english. We need to clarify this

[anastasiia]

These changes after that my slides dissapeared and the data was changed, were made by an anonymous user on 10.01.2019 at 3:50 PM. I am wondering if there is an explanation for this.