https://github.com/ulelab/bs_assign

Find groups of motifs around genomic landmarks of interest
https://github.com/ulelab/bs_assign

bioinformatics bioinformatics-analysis bioinformatics-scripts

Last synced: 4 months ago
JSON representation

Find groups of motifs around genomic landmarks of interest

• Host: GitHub
• URL: https://github.com/ulelab/bs_assign
• Owner: ulelab
• License: gpl-3.0
• Created: 2021-06-30T08:50:15.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2023-09-29T07:57:50.000Z (over 2 years ago)
• Last Synced: 2025-09-05T01:32:27.477Z (9 months ago)
• Topics: bioinformatics, bioinformatics-analysis, bioinformatics-scripts
• Language: Python
• Homepage:
• Size: 34.2 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

Awesome Lists containing this project

README

          
## bs_assign

Author: aram.amalietti@gmail.com

[![DOI](https://zenodo.org/badge/381635264.svg)](https://zenodo.org/badge/latestdoi/381635264)

**Dependencies** (these are the versions the script was developed with, newer versions should work, but if they don't, please use these versions):

```

python=3.7  

pandas=1.2.3  

numpy=1.19.2  

pybedtools=0.8.1  

iteration_utilities=0.11.0  

```

**Usage**:  

  ```

  python3              

  ```  

  `motif1,motif2,...motifn` *is the group of motifs that is searched for around the landmarks, for example AAAA,CCCC,GGGG;* 

  `xl_in` *is a BED file with landmarks around which the motifs are being searched for;*   

  `prtxn` *is the path to the file containing relevant positions where the motif needs to be in order to be detected, it is an output from another script, PEKA;*  

  `fasta` *is the path to the genome in fasta format;*  

  `fai` *is the path to the genome index file;*  

  `window` *is the flanking distance in bases around the landmarks (one base) within which the motifs are being searched for (30 is the usual value);*  

  `len` *is the length of the motifs (4-7 is the usual range);*  

  `cores` *is the number of threads used in the process;*  

  `chunk_size` *is the number of rows per thread (10000 is the usual value);*  

  `output_dir` *is the directory where the results will be saved (make sure it exists);*  

  `consensus` *is a meta motif representing the motif group and will be used in output file names;*  

  Optionally this script can be ran without prtxn file and in that case it will use all the motifs found around crosslinks instead of only those on positions defined in prtxn file.

  

**Outputs**:

 BED files representing the binding sites found within the given window around the given landmarks, binding sites are basically found motifs merged.  

 There are two merging distances and two corresponding files, one is merged0 representing merging distance 0 and the other merged30 for 30.