STREAM is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=16g -c14 [user@@cn3107 ~]$ module load STREAM [user@@cn3107 ~]$ cp $STREAM_DATA/* . [user@@cn3107 ~]$ stream -m data_Guo.tsv.gz -l cell_label.tsv.gz -c cell_label_color.tsv.gz -g gene_list.tsv.gz -s all _____ _______ _____ ______ __ __ / ____|__ __| __ \| ____| /\ | \/ | | (___ | | | |__) | |__ / \ | \ / | \___ \ | | | _ /| __| / /\ \ | |\/| | ____) | | | | | \ \| |____ / ____ \| | | | |_____/ |_| |_| \_\______/_/ \_\_| |_| - Single-cell Trajectory Reconstruction and Mapping - [Luca Pinello & Huidong Chen 2018, send bugs, suggestions or comments to lucapinello AT gmail DOT com] Version 0.1.0 Loading input data... Input: 271 cells, 175 genes Filtering genes... After filtering out low-expressed genes: 271 cells, 172 genes Number of CPUs being used: 56 Reducing dimension... Structure Learning... Clustering... Minimum Spanning Tree... Number of initial branches: 5 Elastic Principal Graph... [1] "Constructing tree 1 of 1 / Subset 1 of 1" [1] "Computing EPG with 50 nodes on 271 points and 3 dimensions" [1] "Using a single core" Nodes = 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD 2||50 0.000668 50 49 44 2 0 0 0.0002886 0.0002736 0.974 0.9754 0.000344 3.539e-05 0.001769 0.08846 0 13.16 sec elapsed [[1]] Number of branches after initial ElPiGraph: 5 Collasping small branches ... [1] "Constructing tree 1 of 1 / Subset 1 of 1" [1] "Computing EPG with 80 nodes on 271 points and 3 dimensions" [1] "Using a single core" Nodes = 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 BARCODE ENERGY NNODES NEDGES NRIBS NSTARS NRAYS NRAYS2 MSE MSEP FVE FVEP UE UR URN URN2 URSD 2||80 0.0004009 80 79 74 2 0 0 0.0001989 0.0001921 0.9821 0.9827 0.0001738 2.82e-05 0.002256 0.1805 0 4.812 sec elapsed Number of branches after optimization: 5 Extending leaves with additional nodes ... Number of branches after extension: 5 Visualizing cells... Flat tree plots... /opt/conda/lib/python2.7/site-packages/networkx/drawing/nx_pylab.py:520: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. if not cb.is_string_like(edge_color) \ /opt/conda/lib/python2.7/site-packages/networkx/drawing/nx_pylab.py:524: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. for c in edge_color]): /opt/conda/lib/python2.7/site-packages/networkx/drawing/nx_pylab.py:722: MatplotlibDeprecationWarning: The is_string_like function was deprecated in version 2.1. if not cb.is_string_like(label): Subway map and Stream plots... Visulizing genes... Finished computation...NOTE: in order to download more sample data, use the Dropbox link.
[user@cn3107 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. stream.sh). For example:
#!/bin/bash module load STREAM stream -m data_Guo.tsv.gz -l cell_label.tsv.gz -c cell_label_color.tsv.gz -g gene_list.tsv.gz -s all stream -m data_Nestorowa.tsv.gz -l cell_label.tsv.gz -c cell_label_color.tsv.gz -s all
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] stream.sh