smith-chem-wisc/spritz

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

spritz's Issues

Adjust java memory parameter based on memory of computer

Rework strand-specific inference

Using DotNetBio SAMFlags implementation instead of RSeQC

Fix aptitude dependency check for repo entries that aren't commands

Currently, this is:

                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...

Add spritz integration to Slack channel

Allow combining results of multiple FASTQ pairs

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

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:

1. Load the fasta
2. Check the alphabet

Determine HLA genotype(s)

STAR sometimes fails because of too many open files (due to high thread count)

alexdobin/STAR#269

Might need to catch this error somehow. I can't change the ulimit -n maximum.

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

Improve variant combinatorics

Limited it to 5 variants per transcript for now.

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

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.

Allow UCSC references to be used

Implement UCSCDownloadsWrapper similar to EnsemblDownloadsWrapper

Make installer

Tidying up DLLs

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

Design and make a GUI

Is karyotypic ordering strictly based on the sizes of chromosomes?

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

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

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

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

Use friendly or full chromID for intervals in GeneModel.ReadGeneFeatures()?

SnpEff GRCh38 version mismatches

1. 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.
2. SnpEff includes the transcript version concatenated with a . to the transcript ID for GRCh38.86 and not for GRCh37.75
3. This really makes me want to make the program independent of that output, like I attempted at first.

Add manifest file for long filepaths

See MetaMorpheus

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.

Output XML without combinitorics but with complete SAV annotations

Run bedops, lastz, mfold setups in parallel to speed up

These setups need root permissions. 1) Generate scripts for each, 2) Run sudo bash script.bash & for each to run in parallel with root permissions.

Load references into Spritz directory instead of analysis directory

It can be used for more than one analysis.

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)

Enable downloading of specific versions of commandline programs

Can we find back-spliced translation products?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052039/

Implement HISAT2 instead of TopHat2 for low-RAM alignments

The TopHat website recommends to use HISAT2 instead https://ccb.jhu.edu/software/tophat/index.shtml

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

Download only the programs needed for certain workflows on the fly

This lazy initialization will also help with downloading different versions only when needed (see #60).

In other words, note the dependencies in each workflow, and have ManageToolsFlow download those each time if needed.

Separate AlignmentFlow from Fastq2ProteinsEngine, so that it can be used elsewhere, too

AF is a measure of how common the variant is; GT tells whether it's heterozygous

Porting the VCF reader implementation from SnpEff would be an improvement

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

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.

Run SplitNCigarReads in parallel before variant HaplotypeCaller

SplitNCigarReads can't use multiple threads, so run it in parallel for several BAM files to speed things up.

Make cleanup scripts for each wrapper

We should have a way to clean up all of the installed packages and return the bash commandline to the way it was before setting up Spritz.

PLIER integration?

https://github.com/wgmao/PLIER

https://www.biorxiv.org/content/early/2017/03/11/116061

Occasionally stdout freezes when a character is highlighted on the bash terminal

This is a good bug to note in a tutorial vid

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

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

Based on memory and organism being used

Change over to using `wsl` to run silent background processes

https://superuser.com/questions/1167718/running-a-bash-background-process-on-windows-10-without-an-open-terminal

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 ().

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

Set up Jenkins for continuous integration

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

Can we figure out the unknown start/stop codons for putative transcripts from proteomics data?

https://www.biostars.org/p/120617/#121342

Download uniprot database and transfer modifications to ensembl sequences

Already partially implemented in Proteogenomics.ProteinAnnotation

Look through all possible translation of PacBio transcripts, not just the first one to pass min length threshold

Implement lncRNA discovery workflow

using slncky and other tools