Analysis - Tools - RUM

RUM

We use the RUM package from Grant et al to do the basic processing of RNA-Seq data.  RUM generates a set of files which we then process a bit further to make them visible in the TessLA browser and for other down-stream analyses.

Files

Here is a typical set of files produced for a RUM analysis:

26642352304 RUM.sam - all alignments
 9094911272 RUM_NU - non-unique alignments
   48715025 RUM_NU.bedGraph.gz - bedGraph format for display
    1002296 RUM_NU.bedGraph.gz.tbi - index of bedGraph format for display
  213897294 RUM_NU.cov - coverage data for non-uniquely mapping reads
 3687201046 RUM_Unique - unique alignments
   52517756 RUM_Unique.bedGraph.gz  - bedGraph format for display
     830599 RUM_Unique.bedGraph.gz.tbi - index of bedGraph format for display
  228549781 RUM_Unique.cov - coverage data for uniquely mapping reads
  122977785 feature_quantifications-max.tab
  122977785 feature_quantifications-max.tab-sorted
  122977785 feature_quantifications-min.tab
  122977785 feature_quantifications-min.tab-sorted
  111522316 feature_quantifications_RLB-GENOME-TAG - expression levels of transcript, exons, and introns.
    5417514 inferred_internal_exons.bed
    3126115 inferred_internal_exons.txt
   30203897 junctions_all.bed
   30203808 junctions_all.bed-sorted
   18500890 junctions_all.rum
    9149089 junctions_high-quality.bed
    9148994 junctions_high-quality.bed-sorted
      16384 log
       4142 mapping_stats.txt - summary of how many reads mapped to genome or transcripts
     289688 novel_inferred_internal_exons_quantifications_RLB-GENOME-TAG
      16384 postproc
 5438152292 quals.fa - read qualities
 5438152292 reads.fa - read sequences
        449 rum_RLB-GENOME-TAG_preproc.sh
        848 rumRLB-GENOME-TAG_proc.sh
       1837 rum_job_config
       3275 rum_job_report.txt
       1384 rum_runner.log
        125 rum_sge_job_ids