smith-chem-wisc / spritz Goto Github PK

View Code? Open in Web Editor NEW

7.0 5.0 11.0 35.59 MB

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

Home Page: https://smith-chem-wisc.github.io/Spritz/

License: MIT License

C# 53.69% Dockerfile 0.21% Python 46.10%

bioinformatics proteogenomics snakemake snakemake-pipeline rna-seq proteomics

spritz's Introduction

Spritz

Software for RNA-Seq analysis on Windows, including creating sample-specific proteoform databases from genomic data

Spritz can be downloaded here.

Spritz uses snakemake and Docker to install and run commandline tools for Next-Generation Sequencing (NGS) analysis. These tools include an adapted version of SnpEff to annotate sequence variations and create an annotated protein database in XML format. The combinatorics of producing full-length proteoforms from these annotations is written in mzLib's VariantApplication class.

Running Spritz with GUI

Install Docker Desktop for Windows.
Allocate resources to Docker. There are two ways to do this, described in the Spritz wiki:
1. The recommended method requires Windows 10 version 2004 and is more robust. Here, we allocate computer resources to Docker like any other program.
2. The alternate method is available on all Windows versions but is less robust. Here, we allocate computer resources to Docker using a virtual machine that's packaged with Docker.
Launch Spritz.

Step 1: Input SRA accessions and/or add FASTQ files.
- SRAs are added with the button indicating single-end or paired-end.
- FASTQ files must end with *_1.fastq if single-end, and paired-end sequences must have the same filename other than ending with *_1.fastq and *_2.fastq.
Step 2: Create and customize your Spritz workflow.

Step 3: Run Spritz!

GUI System Requirements

Environment:
- Windows 10 recommended
- .NET Core 6.0
24 GB RAM recommended
The installer (Spritz.msi) only works on Windows.

Running Spritz with commandline

Spritz will also work on the commandline within a Unix system (Linux, Mac, WSL on Windows).

Test it out! Try constructing the database for U2OS from the paper.

Add SRR629563 to the SRA list.
Create the Spritz workflow. Select "release-97" and "homo_sapiens."
Run Spritz!

Monitor progress in the Information textbox. The final database named final/combined.spritz.snpeff.protein.withmods.xml.gz can be used to search MS/MS with MetaMorpheus to find variant peptides and proteoforms, possibly with modifications. We recommend performing 1) Calibration, 2) Global PTM Discovery (G-PTM-D), and 3) Search tasks to get the best results.

The final database named final/combined.spritz.snpeff.protein.fasta is generated to contain variant protein sequences, and it may be used in other search software, such as Proteome Discoverer, ProSight, and MASH Explorer.

The final database named final/combined.spritz.snpeff.protein.withdecoys.fasta is ready for use in MSFragger. It is generated to contain variant protein sequences with decoy protein sequences appended.

Citations

If you use this Spritz, please cite:

Spritz: Cesnik, A. J.; Miller, R. M.; Ibrahim, K.; Lu, L.; Millikin, R. J.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. “Spritz: A Proteogenomic Database Engine.” J. Proteome Res. 2021, 20, 4, 1826–1834. https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00407

This pipeline uses the following tools:

sra-toolkit: Leinonen, R.; et al. International Nucleotide Sequence Database Collaboration. The Sequence Read Archive. Nucleic Acids Res. 2011, 39 (Database issue), D19-21. https://doi.org/10.1093/nar/gkq1019.
fastp: Chen, S.; et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018, 34 (17), i884-i890. https://academic.oup.com/bioinformatics/article/34/17/i884/5093234
hisat2: Kim, D.; et al. Graph-Based Genome Alignment and Genotyping with HISAT2 and HISAT-Genotype. Nat. Biotechnol. 2019, 37 (8), 907-915. https://doi.org/10.1038/s41587-019-0201-4."
samtools: Li, H.; et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25 (16), 2078-2079. https://academic.oup.com/bioinformatics/article/25/16/2078/204688.
GATK: McKenna, A.; et al. The Genome Analysis Toolkit: A MapReduce Framework for Analyzing next-Generation DNA Sequencing Data. Genome Res. 2010, 20 (9), 1297-1303. https://doi.org/10.1101/gr.107524.110.
SnpEff: Cingolani, P.; et al. A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila Melanogaster Strain W1118; Iso-2; Iso-3. Fly (Austin) 2012, 6 (2), 80-92. https://doi.org/10.4161/fly.19695.
StringTie2: Kovaka, S.; et al. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol 2019, 20 (278), 1-13. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1910-1

spritz's People

Contributors

Stargazers

Watchers

Forkers

acesnik rmmiller22 bintiibrahim cullanm inambioinfo trishorts jokendo-collab tao-su rfellers animesh fullscreen-triangle

spritz's Issues

Load references into Spritz directory instead of analysis directory

It can be used for more than one analysis.

Indicate whether STAR can be used, and use Tophat2 where it's not recommended

Based on memory and organism being used

Write a protein XML with variant information in the XML entry for usage in MetaMorpheus

Porting the VCF reader implementation from SnpEff would be an improvement

Has phasing
Well tested
"VcfEntries" are a bit more intuitive than "VariantContexts"

Rework strand-specific inference

Using DotNetBio SAMFlags implementation instead of RSeQC

Run bash processes in background and wait on them to finish

https://unix.stackexchange.com/questions/340077/how-do-i-wait-for-a-background-process-to-complete

Make installer

Implement advanced options for RSEM and low-RAM RSEMBowtie

Defaults are probably okay, but there are some advanced options:

    --fragment-length-min <int>
        Minimum read/insert length allowed. This is also the value for the
        Bowtie/Bowtie2 -I option. (Default: 1)

    --fragment-length-max <int>
        Maximum read/insert length allowed. This is also the value for the
        Bowtie/Bowtie 2 -X option. (Default: 1000)

    --fragment-length-mean <double>
        (single-end data only) The mean of the fragment length distribution,
        which is assumed to be a Gaussian. (Default: -1, which disables use of
        the fragment length distribution)

    --fragment-length-sd <double>
        (single-end data only) The standard deviation of the fragment length
        distribution, which is assumed to be a Gaussian. (Default: 0, which
        assumes that all fragments are of the same length, given by the
        rounded value of --fragment-length-mean)

Tidying up DLLs

https://stackoverflow.com/a/2445590/9454443

Set up Jenkins for continuous integration

We can't use AppVeyor because the tests need to use Windows Subsystem for Linux

Implement a transfer FDR calculation for TopHat novel splice junction peptides, since they're low #identifications

http://www.ncbi.nlm.nih.gov/pubmed/24200586

Figure out a way in GUI to allow user to choose non-human Ensembl download options

Design and make a GUI

Depth cutoff for heterozygyous missense SNVs?

Showed that depth cutoffs work to improve FDR for peptide identification in 10 cell lines paper
Apply cutoff to both alleles in heterozygous variations?
Heterozygous variation is included if any reads are found for the heterozygous allele, currently. This could be problematic. See https://github.com/acesnik/Bio.VCF/blob/master/VCF/GenotypeContext/Genotype.cs#L329.

Possible install problem of STAR

The /CMD/bin/Debug/STAR file is empty after the first time setup. (Both in Orion or LEI)
Delete the STAR directory, then setup again will install STAR successfully.
Related to STARWrapper.cs Line 184.

A bug only in LEI. a /CMD/bin/Debug/bin directory contain something in /CMD/bin/Debug/bedops are not remove somehow

Is karyotypic ordering strictly based on the sizes of chromosomes?

That would make Genome.KaryotypicOrder() and Genome.IsKaryotypic() much easier!

Display output files in Spritz GUI as they are created/closed

The flow will generate multiple types of files (eg. STAR2PassAlignFLow.AlignFastqs have a lot of string path include index, sam file bam file...). I prefer to set those string path as constant ().

Improve applying variants

Make Interval, Marker, and IntervalAndSubInterval<T> classes like SnpEff, which have nice methods for applying variants. Interval can use SequenceRange from DotNetBio, since it's already comparable. Markers, a collection of Marker objects can be SequenceRangeGrouping, a collection of SequenceRange objects that allows intersecting and such.

The key goal here is applying SNPs, MNPs, and indels in a tidy way.

More useful commandline interface output

There's more functionality we can implement for commandline output:
https://github.com/commandlineparser/commandline/wiki.

I especially like notes of error messages regarding the commandline input.

Validation of fasta files before adding to genome fasta or protein fasta lists

Important for the GUI. We can use the BioDotNet framework for this:

Load the fasta
Check the alphabet

Make these 5 heterozygous, not just 5 variants
Phase nearby variants

When deleting a directory and having a bash terminal open to that directory, the listings for spawned processes in bash are not updated

Use sanityCheck() to figure out bad transcript accessions instead of looking into pep.all.fasta?

SnpEff GRCh38 version mismatches

It turns out the databases that SnpEff uses are GRCh38.86, not GRCh38.81 like I've been using. Most of the transcript IDs are probably the same, but there are likely some that changed.
SnpEff includes the transcript version concatenated with a . to the transcript ID for GRCh38.86 and not for GRCh37.75
This really makes me want to make the program independent of that output, like I attempted at first.

                commands.Add
                (
                    "if commmand -v " + dependency + " > /dev/null 2>&1 ; then\n" +
                    "  echo found\n" +
                    "else\n" +
                    "  sudo apt-get -y install " + dependency + "\n" +
                    "fi"
                );

It should be something that checks for the apt dependency, not the command...

Implement lncRNA discovery workflow

using slncky and other tools