Last updated: 2018-08-30

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    File Version Author Date Message
    Rmd a5f5276 Briana Mittleman 2018-08-30 initialize diff iso pipeline

In my early analysis of the first 32 libraries I ran the leafcutter differential isoform tool. I am now going to rerun this with the peaks called from the 28 individuals. These peaks have been created with the Peak pipeline in https://brimittleman.github.io/threeprimeseq/peak.cov.pipeline.html. These are also the peaks used for the initial QTL analysis. https://brimittleman.github.io/threeprimeseq/apaQTLwLeafcutter.html. I can use the same phenotype and genotype files from this analysis.

To run the differential isoform analysis I need a file with the lines numbers and the fraction. This is similar to the sample.txt file from the QTL analysis.

The phenotype file is filtered_APApeaks_merged_allchrom_refseqGenes_pheno.txt. I can use the header of this to create the sample form. I will work in the directory: /project2/gilad/briana/threeprimeseq/data/diff_iso/

make_samplegroups.py


outfile=open("/project2/gilad/briana/threeprimeseq/data/diff_iso/sample_groups.txt", "w")
infile=open("/project2/gilad/briana/threeprimeseq/data/diff_iso/filtered_APApeaks_merged_allchrom_refseqGenes_pheno.txt", "r")

for ln, i in enumerate(infile):
    if ln==0:
        header=i.split()
        lines=header[1:]
        for l in lines:
            if l[-1] == "T":
                outfile.write("%s\tTotal\n"%(l))
            else:

                outfile.write("%s\tNuclear\n"%(l))
                
outfile.close()

I can now run the leafcutter_ds.R file.

run_leafcutter_ds.sh

#!/bin/bash

#SBATCH --job-name=diff_isoTN
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=diff_isoTN.out
#SBATCH --error=diff_isoTN.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END


module load R  


Rscript /project2/gilad/briana/threeprimeseq/data/diff_iso/leafcutter_ds.R /project2/gilad/briana/threeprimeseq/data/diff_iso/filtered_APApeaks_merged_allchrom_refseqGenes_pheno.txt /project2/gilad/briana/threeprimeseq/data/diff_iso/sample_groups.txt -o /project2/gilad/briana/threeprimeseq/data/diff_iso/TN_diff_isoform

Error in dimnames(x) <- dn : length of ‘dimnames’ [2] not equal to array extent Calls: differential_splicing -> get_intron_meta -> colnames<- Execution halted

Problem may be due to the phenotype file. It looks like the header does not need a PeakID column.

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.18      digest_0.6.16    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.11    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

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