Last updated: 2020-03-27

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
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    Modified:   analysis/upsetter_DF.Rmd

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Rmd f92b89c brimittleman 2020-03-26 add ortho exon and new mm

I want to look at the parameters for multimapping. I will look at the paremeters such as include a read when the first vs second map difference is 10%, 5% ect. I want to get to a cutoff where the PAS lost are not in the ortho exon.

I will look at the featurecounts documentation for this or I can look directly at the star info.

−−primary: If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in the Flag field of SAM/BAM files. All primary alignments in a dataset will be counted no matter they are from multi- mapping reads or not (ie. ‘-M’ is ignored).

For multi-mappers, all alignments except one are marked with 0x100 (secondary alignment) in the FLAG (column 2 of the SAM

I used options:

–outFilterMultimapNmax 10 –outSAMmultNmax 1

–outSAMmultNmax 1 will output exactly one SAM line for each mapped read

I only allowed for 1 read to be mapped. I want the secondary one as well. I want to mess with the secondary read.

Remap human and chimp reads with the new filter. Just to look first, don’t worry about misspriming.

mkdir ../data/TestMM2/
sbatch StarMM2.sh

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] workflowr_1.6.0 Rcpp_1.0.2      digest_0.6.18   later_0.7.5    
 [5] rprojroot_1.3-2 R6_2.3.0        backports_1.1.2 git2r_0.26.1   
 [9] magrittr_1.5    evaluate_0.12   stringi_1.2.4   fs_1.3.1       
[13] promises_1.0.1  whisker_0.3-2   rmarkdown_1.10  tools_3.5.1    
[17] stringr_1.3.1   glue_1.3.0      httpuv_1.4.5    yaml_2.2.0     
[21] compiler_3.5.1  htmltools_0.3.6 knitr_1.20