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YeoLab / rbp-maps

splicing and feature maps for RBPs
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heatmap is empty with se entropy normalization #4

Closed ecwheele closed 7 years ago

ecwheele commented 7 years ago

Command:

/home/bay001/projects/codebase/rbp-maps/maps/plot_density.py --ip /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW34_SRSF2_n212_diff_IP.merged.r2.bam --input /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW_diff_input_master_R1.adapterTrim.round2.rmRep.rmDup.sorted.r2.bam --annotations /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_unchanged_SE.txt --annotation_type rmats rmats rmats --output /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/rbpmaps_encode/se_entropy/EW34_SRSF2_n212_diff_IP.svg --event se --normalization_level 2 --chrom_sizes /projects/ps-yeolab/genomes/hg19/hg19.chrom.sizes

output looks like this:

screen shot 2017-08-14 at 12 27 46 pm

ecwheele commented 7 years ago

Also this warning message is thrown:


/home/ecwheele/anaconda2/envs/rbp-maps/lib/python2.7/site-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "```
byee4 commented 7 years ago

what do the intermediate files look like (what are the intermediate files produced?)

On Mon, Aug 14, 2017 at 1:27 PM, Emily Wheeler notifications@github.com wrote:

Command:

/home/bay001/projects/codebase/rbp-maps/maps/plot_density.py --ip /projects/ps-yeolab3/clip_notencode/ecwheele/20170614 SRSF2_eirini_all_clip/pipeline_output_v1/EW34_SRSF2_n212_diff_IP.merged.r2.bam --input /projects/ps-yeolab3/clip_notencode/ecwheele/20170614 SRSF2_eirini_all_clip/pipeline_output_v1/EWdiff input_master_R1.adapterTrim.round2.rmRep.rmDup.sorted.r2.bam --annotations /projects/ps-yeolab3/ecwheele/20170627_srsf2_allrnaseq eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/ 20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_allrnaseq eirini/rmats/wt_vs_mut_diff_unchanged_SE.txt --annotation_type rmats rmats rmats --output /projects/ps-yeolab3/ecwheele/ 20170627_srsf2_all_rnaseq_eirini/rmats/rbpmaps_encode/ se_entropy/EW34_SRSF2_n212_diff_IP.svg --event se --normalization_level 2 --chrom_sizes /projects/ps-yeolab/genomes/hg19/hg19.chrom.sizes

output looks like this:

[image: screen shot 2017-08-14 at 12 27 46 pm] https://user-images.githubusercontent.com/11878945/29290265-43a448c6-80f4-11e7-8846-89d0248e48ba.png

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ecwheele commented 7 years ago 

-rw-r--r-- 1 ecwheele yeo-group  5876194 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.txt.input.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group  6022791 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.txt.ip.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group  5035985 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.txt.input.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group 10974706 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.txt.ip.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group  9013912 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.txt.input.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group 13665546 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.normed_matrix.txt
-rw-r--r-- 1 ecwheele yeo-group 12787827 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.normed_matrix.txt
-rw-r--r-- 1 ecwheele yeo-group 20715093 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.normed_matrix.txt
-rw-r--r-- 1 ecwheele yeo-group    25011 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.means.txt
-rw-r--r-- 1 ecwheele yeo-group    25056 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.means.txt
-rw-r--r-- 1 ecwheele yeo-group    25057 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.means.txt
-rw-r--r-- 1 ecwheele yeo-group    25048 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.sems.txt
-rw-r--r-- 1 ecwheele yeo-group    25032 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.sems.txt
-rw-r--r-- 1 ecwheele yeo-group    25064 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.sems.txt
-rw-r--r-- 1 ecwheele yeo-group        0 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.zscores.txt
-rw-r--r-- 1 ecwheele yeo-group        0 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.zscores.txt
-rw-r--r-- 1 ecwheele yeo-group        0 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.zscores.txt
-rw-r--r-- 1 ecwheele yeo-group   350430 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.svg```
byee4 commented 7 years ago

Please use the --bgnum and --to_test commands to specify which annotations are used as backgrounds:

/home/bay001/projects/codebase/rbp-maps/maps/plot_density.py --ip /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW34_SRSF2_n212_diff_IP.merged.r2.bam --input /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW_diff_input_master_R1.adapterTrim.round2.rmRep.rmDup.sorted.r2.bam --annotations /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_unchanged_SE.txt --annotation_type rmats rmats rmats --output EW34_SRSF2_n212_diff_IP.svg --event se --normalization_level 2 --chrom_sizes /projects/ps-yeolab/genomes/hg19/hg19.chrom.sizes --bgnum 2 --to_test /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt