A open-source tool for rapid analysis of RNA mutational profiling (MaP) experiments. This tool was inspired by the DREEM algorithm developed by the Rouskin Lab (https://www.rouskinlab.com/). Please cite this work (https://doi.org/10.1093/nar/gkac435).
The MaP analysis web tool provides a simple platform for analyzing DMS-reactivity of an RNA. The user input is a raw sequencing file (.fastq) generated from a DMS-MaPseq experiment, and a sequence of the RNA of interest (.fasta). The DREEM algorithm performs sequence alignment using bowtie-2 and outputs the mismatch rate per nucleotide.
- python 3.8 or greater
- bowtie2 (2.2.9) - https://github.com/BenLangmead/bowtie2/releases/download/v2.2.9/
- trim_galore (0.6.6) - https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.tar.gz
- fastqc (0.11.9) - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
- cutadapt (1.18) - https://github.com/marcelm/cutadapt/archive/refs/tags/v1.18.zip
- conda (optional) - https://docs.anaconda.com/anaconda/install/
- docker (optional) - https://docs.docker.com/get-docker/
If you are trying the software for the first time highly recommended to use the docker image.
Highly recommended to use conda to manage your python environment.
conda create -n rna-map python=3.8
pip install rna-map
# on linux and intel mac
git clone https://github.com/YesselmanLab/rna_map
cd rna_map
pip install .
docker build -t rna-map -f docker/Dockerfile .
# on mac with apple silicon / or other arm64 platforms
docker build -t rna-map --platform linux/amd64 -f docker/Dockerfile .
After installed there will be a new command line tool called rna-map available.
# run in single end mode
rna-map -fa <fasta file> -fq1 <fastq file>
# run in paired end mode
rna-map -fa <fasta file> -fq1 <fastq file> -fq2 <fastq file>
# supply a csv with dot bracket structures. These will apppear in the
# results in plots and pickle file
rna-map -fa <fasta file> -fq1 <fastq file> --dot-bracket <csv file>--docker flag will run the docker image. if you have run docker build first
# run in single end mode
# note this will only work if you built the image with docker command above
rna-map -fa <fasta file> -fq1 <fastq file> --docker
# TODO check is necessary?
# run on apple silicon on / or other arm64 platforms
rna-map -fa <fasta file> -fq1 <fastq file> --docker --docker-platform linux/amd64rna-map --help
Usage: rna-map [OPTIONS]
rapid analysis of RNA mutational profiling (MaP) experiments.
Main arguments:
These are the main arguments for the command line interface
-fa, --fasta PATH The fasta file containing the reference
sequences [required]
-fq1, --fastq1 PATH The fastq file containing the single end reads
or the first pair of paired end reads
[required]
-fq2, --fastq2 TEXT The fastq file containing the second pair of
paired end reads
--dot-bracket TEXT The directory containing the input files
-pf, --param-file TEXT A yml formatted file to specify parameters, see
rna_map/resources/default.yml for an example
-pp, --param-preset TEXT run a set of parameters for specific uses like
'barcoded-libraries'
Mapping options:
These are the options for pre processing of fastq files and alignment to
reference sequences
--skip-fastqc do not run fastqc for quality control of
sequence data
--skip-trim-galore do not run trim galore for quality control of
sequence data
--tg-q-cutoff INTEGER the quality cutoff for trim galore
--bt2-alignment-args TEXT the arguments to pass to bowtie2 for alignment
seperated by commas
--save-unaligned the path to save unaligned reads to
Bit vector options:
These are the options for the bit vector step
--skip-bit-vector do not run the bit vector step
--summary-output-only do not generate bit vector files or plots
recommended when there are thousands of
reference sequences
--plot-sequence plot sequence and structure is supplied under
the population average plots
--map-score-cutoff INTEGER reject any bit vector where the mapping score
for bowtie2 alignment is less than this value
--qscore-cutoff INTEGER quality score of read nucleotide, sets to
ambigious if under this val
--mutation-count-cutoff INTEGER
maximum number of mutations allowed in a bit
vector will be discarded if higher
--percent-length-cutoff FLOAT minium percent of the length of the reference
sequence allowed in a bit vector will be
discarded if lower
--min-mut-distance INTEGER minimum distance between mutations in a bit
vector will be discarded if lower
Docker options:
These are the options for running the command line interface in a docker
container
--docker Run the program in a docker container
--docker-image TEXT The docker image to use
--docker-platform TEXT The platform to use for the docker image
Misc options:
These are the options for the misc stage
--overwrite overwrite the output directory if it exists
--restore-org-behavior restore the original behavior of the rna_map
--stricter-bv-constraints use stricter constraints for bit vector
generation, use at your own risk!
--debug enable debug mode
Other options:
--help Show this message and exit.
rna-map -fa test/resources/case_1/test.fasta -fq1 test/resources/case_unit/test_mate1.fastq -fq2 test/resources/case_unit/test_mate2.fastq rna_map.CLI - INFO -
88888888ba 888b 88 db 88b d88 db 88888888ba
88 "8b 8888b 88 d88b 888b d888 d88b 88 "8b
88 ,8P 88 `8b 88 d8'`8b 88`8b d8'88 d8'`8b 88 ,8P
88aaaaaa8P' 88 `8b 88 d8' `8b 88 `8b d8' 88 d8' `8b 88aaaaaa8P'
88""""88' 88 `8b 88 d8YaaaaY8b 88 `8b d8' 88 d8YaaaaY8b 88""""""'
88 `8b 88 `8b 88 d8""""""""8b 88 `8b d8' 88 d8""""""""8b 88
88 `8b 88 `8888 d8' `8b 88 `888' 88 d8' `8b 88
88 `8b 88 `888 d8' `8b 88 `8' 88 d8' `8b 88
rna_map.CLI - INFO - ran at commandline as:
rna_map.CLI - INFO - /Users/jyesselm/miniconda3/envs/py3/bin/rna-map -fa test/resources/case_1/test.fasta -fq1 test/resources/case_unit/test_mate1.fastq -fq2 test/resources/case_unit/test_mate2.fastq
rna_map.RUN - INFO - fasta file: test/resources/case_1/test.fasta exists
rna_map.RUN - INFO - found 1 valid reference sequences in test/resources/case_1/test.fasta
rna_map.RUN - INFO - fastq1 file: test/resources/case_unit/test_mate1.fastq exists
rna_map.RUN - INFO - fastq2 file: test/resources/case_unit/test_mate2.fastq exists
rna_map.RUN - INFO - two fastq files supplied, thus assuming paired reads
rna_map.MAPPING - INFO - bowtie2 2.4.5 detected!
rna_map.MAPPING - INFO - fastqc v0.11.9 detected!
rna_map.MAPPING - INFO - trim_galore 0.6.6 detected!
rna_map.MAPPING - INFO - cutapt 1.18 detected!
rna_map.MAPPING - INFO - building directory structure
rna_map.MAPPING - INFO - bowtie2 2.4.5 detected!
rna_map.MAPPING - INFO - fastqc v0.11.9 detected!
rna_map.MAPPING - INFO - trim_galore 0.6.6 detected!
rna_map.MAPPING - INFO - cutapt 1.18 detected!
rna_map.EXTERNAL_CMD - INFO - running fastqc
rna_map.EXTERNAL_CMD - INFO - fastqc ran without errors
rna_map.EXTERNAL_CMD - INFO - running trim_galore
rna_map.EXTERNAL_CMD - INFO - trim_galore ran without errors
rna_map.EXTERNAL_CMD - INFO - running bowtie2-build
rna_map.EXTERNAL_CMD - INFO - bowtie2-build ran without errors
rna_map.EXTERNAL_CMD - INFO - running bowtie2 alignment
rna_map.EXTERNAL_CMD - INFO - bowtie2 alignment ran without errors
rna_map.EXTERNAL_CMD - INFO - results for bowtie alignment:
25 reads; of these:
25 (100.00%) were paired; of these:
1 (4.00%) aligned concordantly 0 times
24 (96.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
96.00% overall alignment rate
rna_map.MAPPING - INFO - finished mapping!
rna_map.BIT_VECTOR - INFO - starting bitvector generation
rna_map.BIT_VECTOR - INFO - REMOVED READS:
| name | low_mapq |
|---------------|------------|
| mttr-6-alt-h3 | 0 |
rna_map.BIT_VECTOR - INFO - MUTATION SUMMARY:
| name | reads | aligned | no_mut | 1_mut | 2_mut | 3_mut | 3plus_mut | sn |
|---------------|---------|-----------|----------|---------|---------|---------|-------------|------|
| mttr-6-alt-h3 | 24 | 100 | 50 | 33.33 | 12.5 | 4.17 | 0 | 4.91 |- [ ]
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