guertinlab/tn5bias

seqOutATACBias: Rule Ensemble Modeling of seqOutBias Scaling

This GitHub repo contains all of the code and information produced for the Guertinlab Tn5 bias correction project. It was made to accompany the paper "Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling" by providing the code and methods used to produce the figures and data. It is divided into 4 sections:

seqOutATACBias_setup

The folder labeled 'seqOutATACBias_setup' contains seqOutATACBias, which is a CLI that corrects the sequence bias of Tn5 transposase in ATAC-seq data using a rule ensemble model.

seqOutATACBias_workflow_Vignette

The folder labeled 'seqOutATACBias_workflow_Vignette' contains a vignette which explains the methods used by seqOutATACBias and uses data from chromosome 21 to show bias correction. This is a light weight analysis that can be conducted in less than 15 minutes, and uses less than 1Gb of disk space when completed.

Manuscript_Vignette

The folder labled 'Manuscript_Vignette' contains all of the code to conduct the analysis outlined in "Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling". This vignette will download all of the publicly available data used in the paper and conduct the appropriate analysis. Completion takes several days and requires the use of an HPC environment and slightly more than a terabyte of storage space.

Manuscript_Figures

The 'Manuscript_Figures' folder contains the data which is directly plotted in "Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling" figures and the necessary code to produce said figures.

tn5bias's Issues

genome.fa command not found

Hello!

First of all, thank you for your great work!

I was wondering if you could help me with the following error

/usr/bin/bash: line 1: GRCz11.fa: command not found

I am getting it when running the command

seqOutATACBias masks -i=$BAM -g=GRCz11.fa -p=1 -r=50 -c=NO

Is this a bug? How could I solve it?

Thanks in advance.

Issue with compiling code. error[E0310] for rustc-serialize-0.3.23

Hello, I am a very new to rust person and I have been trying to compile seqOutBias to follow along with the vignette for ATAC-seq bias correction. I cannot get the build to work with my computer. I pasted the errors below. Is this something you can help me with?

....
Compiling num-traits v0.1.37
error[E0310]: the parameter type T may not live long enough
--> /home/reneem/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rustc-serialize-0.3.23/src/serialize.rs:1155:5
|
1155 | fn decode<D: Decoder>(d: &mut D) -> Result<Cow<'static, T>, D::Error> {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| |
| the parameter type T must be valid for the static lifetime...
| ...so that the type T will meet its required lifetime bounds...
|
note: ...that is required by this bound
--> /tmp/rust-20240717-30535-cax4sv/rustc-1.79.0-src/library/alloc/src/borrow.rs:180:30
help: consider adding an explicit lifetime bound
|
1151 | impl<'a, T: ?Sized + 'static> Decodable for Cow<'a, T>
| +++++++++

Compiling strsim v0.5.2
Compiling rust-htslib v0.12.1
Compiling flate2 v0.2.18
Compiling tempfile v2.2.0
For more information about this error, try rustc --explain E0310.
error: could not compile rustc-serialize (lib) due to 1 previous error
warning: build failed, waiting for other jobs to finish...

Best,

reneeisnowhere