Results

The minimal polymer length of 2, set in the min_lenght paremeter of the nextflow.config file, is for the homopol_summary.tsv file only (except the two last columns of this file).

Randomisation of each sequence was performed 10,000 times without any constrain. Then means were computed for each homopolymer length category.



Dot plot


Each dot is a value obtained for one sequence.
See the plot_raw_values.tsv file for the plot raw values.

Figure 1: Proportions of homopolymer lengths. See the scatterplot_stat.tsv file for values

Figure 1: Proportions of homopolymer lengths. See the scatterplot_stat.tsv file for values

Figure 2: Proportions of homopolymer lengths (log10)

Figure 2: Proportions of homopolymer lengths (log10)



Boxplot plot


Each dot is a value obtained for one sequence.

Figure 3: Proportions of homopolymer lengths: diamond, mean; whiskers, 1.5 x Inter Quartile Range; horizontal bars, quartiles; number at the top, mean. See the boxplot_stat.tsv file for values

Figure 3: Proportions of homopolymer lengths: diamond, mean; whiskers, 1.5 x Inter Quartile Range; horizontal bars, quartiles; number at the top, mean. See the boxplot_stat.tsv file for values

Figure 4: Proportions of homopolymer lengths (log10)

Figure 4: Proportions of homopolymer lengths (log10)



T test Obs versus Theo for each homopolymer length (see also the t_test.tsv file)

See also the t_test.tsv file.

length obs_mean theo_mean obs_sd theo_sd df t p.value BH.adj.p.value
01 0.229166666666667 0.802950956661501 0.157747454050008 0.00828434936470266 3.0165477915132 -7.2647090476186 0.00528339310285068 0.0211335724114027
02 0.645833333333333 0.187575628908654 0.307129783159666 0.0124818212833651 3.00990973678908 2.98166939316191 0.0582762434926234 0.116552486985247
03 0.0625 0.00837948666658332 0.125 0.0167589733331666 3.10781662731246 0.85824895163558 0.451856906885527 0.451856906885527
04 0.0625 0.00109392776326153 0.125 0.00218785552652306 3.00183809716059 0.982346696573283 0.39832626425463 0.451856906885527



Backup

See the reports folder for all the details of the analysis, including the parameters used in the .config file

Full .nextflow.log is in: /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer
The one in the reports folder is not complete (miss the end)



Workflow Version

General

Variable Value
Project
(empty means no .git folder where the homopolymer.nf file is present)		 origin :gmillot/homopolymer.git (fetch)
Git info
(empty means no .git folder where the homopolymer.nf file is present)		 v5.0-dirty
Cmd line nextflow run main.nf -resume
execution mode local
Manifest’s pipeline version null
result path /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer/results/homopolymer_2_1708366715
nextflow version 23.04.4



Implicit variables

Name Description Value
launchDir Directory where the workflow is run /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer
nprojectDir Directory where the homopolymer.nf script is located /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer
workDir Directory where tasks temporary files are created /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer/work



User variables

Name Description Value
out_path output folder path /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer/results/homopolymer_2_1708366715
in_path input folder path /mnt/c/Users/gmillot/Documents/Git_projects/homopolymer/dataset/test.fasta



Workflow diagram

See the nf_dag.png file