Moving updates to a new repo https://github.com/YesselmanLab/rna_map.
DREEM processes DMS next-generation sequencing data to produce mutational profiles that relate to DMS modification rates written by Silvi Rouskin and the Rouskin lab (https://www.rouskinlab.com/)
The easiest way to install is via docker!
If you are not familiar with docker https://docs.docker.com/get-docker/
# get the code and install the python module
wget https://github.com/jyesselm/dreem/archive/refs/tags/0.2.0.zip && \
unzip 0.2.0.zip && \
mv dreem-0.2.0 dreem && \
cd dreem && \
sudo python3 setup.py install && \
pip install . && \
pip install -r requirements.txt
# to setup the docker image you can either pull
docker pull jyesselm/dreem:latest
# or build docker image from scratch
docker build -t dreem -f docker/Dockerfile .
If you want to run natively DREEM requires:
bowtie2=v2.2.9 (https://github.com/BenLangmead/bowtie2/releases/download/v2.2.9/)
fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
cutapt=v1.18 (https://github.com/marcelm/cutadapt/archive/refs/tags/v1.18.zip)
TrimGalore=v0.6.6 (https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.tar.gz)
I also highly recommend using anaconda for installing all required python packages which are all in requirements.txt
colorlog
click
click-option-group
biopython
plotly
matplotlib
pandas
tabulate
pyyamlmain excutable is dreem after installing locally it should be available in $PATH
Usage: run.py [OPTIONS]
DREEM processes DMS next generation sequencing data to produce mutational
profiles that relate to DMS modification rates written by Silvi Rouskin and
the Rouskin lab (https://www.rouskinlab.com/)
Options:
main arguments:
-fa, --fasta PATH reference sequences in fasta format
[required]
-fq1, --fastq1 PATH fastq sequencing file of mate 1 [required]
-fq2, --fastq2 PATH fastq sequencing file of mate 2
common options:
--dot_bracket PATH A csv formatted file that contains dot
bracket info for each sequence
-pf, --param-file PATH A yml formatted file to specify parameters
-ow, --overwrite overwrites previous results, if not set will
keep previous calculation checkpoints
-ll, --log-level TEXT set log level (INFO|WARN|DEBUG|ERROR|FATAL)
-rob, --restore_org_behavior retores the original behavior of dreem upon
first release
map options:
--map-overwrite overwrite mapping calculation
--skip do not perform sequence mapping, not
recommended
--skip_fastqc do not run fastqc for quality control of
sequence data
--skip_trim_galore do not run trim galore to remove adapter
sequences at ends
--tg_q_cutoff TEXT TODO
--bt2_alignment_args TEXT TODO
bv options:
--skip skip bit vector generation step, not
recommended
--bv-overwrite overwrite bit vector calculation
--qscore_cutoff TEXT quality score of read nucleotide, sets to
ambigious if under this val
--num_of_surbases TEXT number of bases around a mutation
--map_score_cutoff TEXT map alignment score cutoff for a read, read
is discarded if under this value
--mutation_count_cutoff TEXT maximum number of mutations in a read
allowable
--percent_length_cutoff TEXT read is discarded if less than this percent
of a ref sequence is included
--help Show this message and exit.If running through docker you can use all the same arguments but use the exe dreem-docker
There is example data within the dreem/test directory
cd dreem/
dreem -fa test/resources/case_1/test.fasta -fq1 test/resources/case_1/test_mate1.fastq -fq2 test/resources/case_1/test_mate2.fastqsuccessful output looks as follows
[16:08 bit_vector.py main] INFO ran at commandline as:
[16:08 bit_vector.py main] INFO /Users/josephyesselman/installs/anaconda3/envs/py3/bin/dreem -fa test/resources/case_1/test.fasta -fq1 test/resources/case_1/test_mate1.fastq -fq2 test/resources/case_1/test_mate2.fastq
[16:08 bit_vector.py validate_files] INFO fasta file: test/resources/case_1/test.fasta exists
[16:08 bit_vector.py validate_files] INFO fastq file: test/resources/case_1/test_mate1.fastq exists
[16:08 bit_vector.py validate_files] INFO fastq2 file: test/resources/case_1/test_mate2.fastq exists
[16:08 bit_vector.py validate_files] INFO two fastq files supplied, thus assuming paired reads
[16:08 bit_vector.py build_directories] INFO building directory structure
[16:08 mapper.py __init__] INFO bowtie2 2.4.1 detected!
[16:08 mapper.py __init__] INFO fastqc v0.11.9 detected!
[16:08 mapper.py __init__] INFO trim_galore 0.6.6 detected!
[16:08 mapper.py __init__] INFO cutapt 1.18 detected!
[16:08 mapper.py __run_command] INFO running fastqc
[16:08 mapper.py __run_command] INFO fastqc ran without errors
[16:08 mapper.py __run_command] INFO running trim_galore
[16:08 mapper.py __run_command] INFO trim_galore ran without errors
[16:08 mapper.py __run_command] INFO running bowtie2-build
[16:08 mapper.py __run_command] INFO bowtie2-build ran without errors
[16:08 mapper.py __run_command] INFO running bowtie2 alignment
[16:08 mapper.py __run_command] INFO bowtie2 alignment ran without errors
[16:08 mapper.py __run_bowtie_alignment] INFO results for bowtie alignment:
2500 reads; of these:
2500 (100.00%) were paired; of these:
168 (6.72%) aligned concordantly 0 times
2331 (93.24%) aligned concordantly exactly 1 time
1 (0.04%) aligned concordantly >1 times
93.28% overall alignment rate
[16:08 mapper.py __run_picard_bam_convert] INFO Converting BAM file to SAM file format
[16:08 mapper.py __run_command] INFO running picard BAM conversion
[16:08 mapper.py __run_command] INFO picard BAM conversion ran without errors
[16:08 mapper.py __run_picard_sort] INFO sorting BAM file
[16:08 mapper.py __run_command] INFO running picard BAM sort
[16:08 mapper.py __run_command] INFO picard BAM sort ran without errors
[16:08 mapper.py run] INFO finished mapping!
[16:08 sam.py run] INFO starting bitvector generation
[16:08 sam.py __run_command] INFO running picard SAM convert
[16:08 sam.py __run_command] INFO picard SAM convert ran without errors
[16:08 sam.py run] INFO MUTATION SUMMARY
| name | reads | aligned | no_mut | 1_mut | 2_mut | 3_mut | 3plus_mut |
|---------------|---------|-----------|----------|---------|---------|---------|-------------|
| mttr-6-alt-h3 | 2332 | 2331 | 46.42 | 36.81 | 13.21 | 3.05 | 0.04 |
The same command can be run through docker
cd dreem/
dreem-docker -fa test/resources/case_1/test.fasta -fq1 test/resources/case_1/test_mate1.fastq -fq2 test/resources/case_1/test_mate2.fastqoutput as follows
[16:12 RUN_DOCKER main] INFO DOCKER CMD:
docker run -v /Users/josephyesselman/projects/dreem/test/resources/case_1/test.fasta:/data/test.fasta -v /Users/josephyesselman/projects/dreem/test/resources/case_1/test_mate1.fastq:/data/test_mate1.fastq -v /Users/josephyesselman/projects/dreem/test/resources/case_1/test_mate2.fastq:/data/test_mate2.fastq --name dreem_cont -t dreem dreem -fa test.fasta -fq1 test_mate1.fastq -fq2 test_mate2.fastq --log-level INFO
[21:12 bit_vector.py main] INFO ran at commandline as:
[21:12 bit_vector.py main] INFO /opt/conda/envs/py3/bin/dreem -fa test.fasta -fq1 test_mate1.fastq -fq2 test_mate2.fastq --log-level INFO
[21:12 bit_vector.py validate_files] INFO fasta file: test.fasta exists
[21:12 bit_vector.py validate_files] INFO fastq file: test_mate1.fastq exists
[21:12 bit_vector.py validate_files] INFO fastq2 file: test_mate2.fastq exists
[21:12 bit_vector.py validate_files] INFO two fastq files supplied, thus assuming paired reads
[21:12 bit_vector.py build_directories] INFO building directory structure
[21:12 mapper.py __init__] INFO bowtie2 2.2.9 detected!
[21:12 mapper.py __init__] INFO fastqc v0.11.4 detected!
[21:12 mapper.py __init__] INFO trim_galore 0.6.6 detected!
[21:12 mapper.py __init__] INFO cutapt 1.18 detected!
[21:12 mapper.py __run_command] INFO running fastqc
[21:12 mapper.py __run_command] INFO fastqc ran without errors
[21:12 mapper.py __run_command] INFO running trim_galore
[21:12 mapper.py __run_command] INFO trim_galore ran without errors
[21:12 mapper.py __run_command] INFO running bowtie2-build
[21:12 mapper.py __run_command] INFO bowtie2-build ran without errors
[21:12 mapper.py __run_command] INFO running bowtie2 alignment
[21:12 mapper.py __run_command] INFO bowtie2 alignment ran without errors
[21:12 mapper.py __run_bowtie_alignment] INFO results for bowtie alignment:
2500 reads; of these:
2500 (100.00%) were paired; of these:
38 (1.52%) aligned concordantly 0 times
2333 (93.32%) aligned concordantly exactly 1 time
129 (5.16%) aligned concordantly >1 times
98.48% overall alignment rate
[21:12 mapper.py __run_picard_bam_convert] INFO Converting BAM file to SAM file format
[21:12 mapper.py __run_command] INFO running picard BAM conversion
[21:12 mapper.py __run_command] INFO picard BAM conversion ran without errors
[21:12 mapper.py __run_picard_sort] INFO sorting BAM file
[21:12 mapper.py __run_command] INFO running picard BAM sort
[21:12 mapper.py __run_command] INFO picard BAM sort ran without errors
[21:12 mapper.py run] INFO finished mapping!
[21:12 sam.py run] INFO starting bitvector generation
[21:12 sam.py __run_command] INFO running picard SAM convert
[21:12 sam.py __run_command] INFO picard SAM convert ran without errors
[21:12 sam.py run] INFO MUTATION SUMMARY
| name | reads | aligned | no_mut | 1_mut | 2_mut | 3_mut | 3plus_mut |
|---------------|---------|-----------|----------|---------|---------|---------|-------------|
| mttr-6-alt-h3 | 2462 | 2333 | 46.55 | 36.69 | 13.2 | 3.04 | 0.04 |
[16:12 RUN_DOCKER main] INFO clean up and copy files from docker
[16:12 RUN_DOCKER main] INFO docker cp dreem_cont:/data/output output
[16:12 RUN_DOCKER main] INFO docker cp dreem_cont:/data/log log
[16:12 RUN_DOCKER main] INFO docker cp dreem_cont:/data/dreem.log dreem.log
[16:12 RUN_DOCKER main] INFO docker rm dreem_cont
dreem_cont