https://github.com/YeoLab/MINES

(m)6A (I)dentification Using (N)anopor(E) (S)equencing
https://github.com/YeoLab/MINES

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(m)6A (I)dentification Using (N)anopor(E) (S)equencing

• Host: GitHub
• URL: https://github.com/YeoLab/MINES
• Owner: YeoLab
• Created: 2019-06-12T22:43:59.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2020-11-25T10:49:01.000Z (about 4 years ago)
• Last Synced: 2024-08-03T23:18:08.775Z (5 months ago)
• Language: Python
• Size: 8.46 MB
• Stars: 18
• Watchers: 3
• Forks: 3
• Open Issues: 21
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-nanopore - MINES - [Python] - [Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base specific resolution](https://rnajournal.cshlp.org/content/early/2019/10/17/rna.072785.119). (Software packages / RNA modification analysis)

README

        
# MINES

(m)6A (I)dentification Using (N)anopor(E) (S)equencing

## Tombo(v1.4) Commands Prior to MINES:

(Only required if fast5s do not already contain fastqs)

tombo preprocess annotate_raw_with_fastqs --fast5-basedir /fast5_dir/ --fastq-filenames Fastqs --overwrite --processes #

tombo resquiggle /fast5_dir/ REF.fa --overwrite --processes #

tombo detect_modifications de_novo --fast5-basedirs /fast5_dir/ --statistics-file-basename Stats_Filename

tombo text_output browser_files --fast5-basedirs /fast5_dir/ --statistics-filename Stats_Filename.tombo.stats --browser-file-basename output_filename --file-types coverage fraction

## MINES Dependencies:

python                    3.7.0  

pandas                    0.23.4  

pybedtools                0.8.0  

numpy*                     1.16.4  

scikit-learn              0.19.2  

bedops                     2.4.35  

## MINES Usage

### Convert Wig Files Into Bed Files.

wig2bed < output_filename.fraction_modified_reads.plus.wig > output_filename.fraction_modified_reads.plus.wig.bed

### cDNA_MINES Example:

python cDNA_MINES.py --fraction_modified output_filename.fraction_modified_reads.plus.wig.bed --coverage output_filename.coverage.plus.bedgraph --output m6A_output_filename.bed --ref REF.fa

### genomic_MINES Example:

python genomic_MINES.py --fraction_modified_plus output_filename.fraction_modified_reads.plus.wig.bed --coverage_plus output_filename.coverage.plus.bedgraph --coverage_minus output_filename.coverage.minus.bedgraph --fraction_modified_minus output_filename.fraction_modified_reads.minus.wig.bed --output m6A_output_filename.bed --ref REF.fa

### Output File Format(bed/tab delimited):

chr,   start,   stop,    5-mer,   unique key,    strand,    fraction modified^,    coverage  

^fraction modified is the value at the identified m6A site. However, the value at this position should be used with caution as the "A" site was found to be a poor predictor of methylation.

## Reference files can be downloaded from:

hg19:http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ File:hg19.fa.gz then run gunzip.  

cDNA:ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/cdna/  File:Homo_sapiens.GRCh38.cdna.all.fa.gz then run gunzip.