Package: rna-map
RNA MAPA 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.Software requirementspython 3.8 or greaterbowtie2 (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.gzfastqc (0.11.9) -https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zipcutadapt (1.18) -https://github.com/marcelm/cutadapt/archive/refs/tags/v1.18.zipconda (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.How to installHighly recommended to use conda to manage your python environment.conda create -n rna-map python=3.8
pip install rna-mapwith docker# on linux and intel macgitclonehttps://github.com/YesselmanLab/rna_mapcdrna_map
pipinstall.

dockerbuild-trna-map-fdocker/Dockerfile.# on mac with apple silicon / or other arm64 platformsdockerbuild-trna-map--platformlinux/amd64-fdocker/Dockerfile.How to usebasic usageAfter installed there will be a new command line tool calledrna-mapavailable.# run in single end moderna-map-fa<fastafile>-fq1<fastqfile># run in paired end moderna-map-fa<fastafile>-fq1<fastqfile>-fq2<fastqfile># supply a csv with dot bracket structures. These will apppear in the# results in plots and pickle filerna-map-fa<fastafile>-fq1<fastqfile>--dot-bracket<csvfile>running with docker--dockerflag 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 aboverna-map-fa<fastafile>-fq1<fastqfile>--docker# TODO check is necessary?# run on apple silicon on / or other arm64 platformsrna-map-fa<fastafile>-fq1<fastqfile>--docker--docker-platformlinux/amd64working with large sets of RNAssee a full list of arguments belowrna-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.running paired end readsrna-map-fatest/resources/case_1/test.fasta-fq1test/resources/case_unit/test_mate1.fastq-fq2test/resources/case_unit/test_mate2.fastqrna_map.CLI-INFO-
88888888ba888b88db88bd88db88888888ba88"8b  8888b     88        d88b            888b         d888        d88b        88      "8b88,8P88`8b88d8'`8b           88`8b       d8'88d8'`8b       88      ,8P88aaaaaa8P'88`8b88d8'  `8b          88 `8b     d8'88d8'  `8b      88aaaaaa8P'88""""88'    88   `8b  88     d8YaaaaY8b         88  `8b   d8'88d8YaaaaY8b88""""""'88    `8b    88    `8b 88    d8""""""""8b        88   `8b d8'88d8""""""""8b8888`8b88`8888d8'        `8b       88    `888'88d8'        `8b   8888      `8b  88      `888  d8'`8b88`8'     88  d8'`8b88rna_map.CLI-INFO-ranatcommandlineas:
rna_map.CLI-INFO-/Users/jyesselm/miniconda3/envs/py3/bin/rna-map-fatest/resources/case_1/test.fasta-fq1test/resources/case_unit/test_mate1.fastq-fq2test/resources/case_unit/test_mate2.fastq
rna_map.RUN-INFO-fastafile:test/resources/case_1/test.fastaexists
rna_map.RUN-INFO-found1validreferencesequencesintest/resources/case_1/test.fasta
rna_map.RUN-INFO-fastq1file:test/resources/case_unit/test_mate1.fastqexists
rna_map.RUN-INFO-fastq2file:test/resources/case_unit/test_mate2.fastqexists
rna_map.RUN-INFO-twofastqfilessupplied,thusassumingpairedreads
rna_map.MAPPING-INFO-bowtie22.4.5detected!
rna_map.MAPPING-INFO-fastqcv0.11.9detected!
rna_map.MAPPING-INFO-trim_galore0.6.6detected!
rna_map.MAPPING-INFO-cutapt1.18detected!
rna_map.MAPPING-INFO-buildingdirectorystructure
rna_map.MAPPING-INFO-bowtie22.4.5detected!
rna_map.MAPPING-INFO-fastqcv0.11.9detected!
rna_map.MAPPING-INFO-trim_galore0.6.6detected!
rna_map.MAPPING-INFO-cutapt1.18detected!
rna_map.EXTERNAL_CMD-INFO-runningfastqc
rna_map.EXTERNAL_CMD-INFO-fastqcranwithouterrors
rna_map.EXTERNAL_CMD-INFO-runningtrim_galore
rna_map.EXTERNAL_CMD-INFO-trim_galoreranwithouterrors
rna_map.EXTERNAL_CMD-INFO-runningbowtie2-build
rna_map.EXTERNAL_CMD-INFO-bowtie2-buildranwithouterrors
rna_map.EXTERNAL_CMD-INFO-runningbowtie2alignment
rna_map.EXTERNAL_CMD-INFO-bowtie2alignmentranwithouterrors
rna_map.EXTERNAL_CMD-INFO-resultsforbowtiealignment:25reads;ofthese:25(100.00%)werepaired;ofthese:1(4.00%)alignedconcordantly0times24(96.00%)alignedconcordantlyexactly1time0(0.00%)alignedconcordantly>1times96.00%overallalignmentrate
rna_map.MAPPING-INFO-finishedmapping!
rna_map.BIT_VECTOR-INFO-startingbitvectorgeneration
rna_map.BIT_VECTOR-INFO-REMOVEDREADS:|name|low_mapq||---------------|------------||mttr-6-alt-h3|0|rna_map.BIT_VECTOR-INFO-MUTATIONSUMMARY:|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|TODOAdd mac build to github actions