Source of every last read

ROP is able to detect the source of every last RNA-Seq read. The reads not mapped to the refference genome might originate from complex RNA molecules, recombinant antibodies and microbial communities. The ROP accounts for 98.8% of all reads across poly(A) and ribo-depletion libraries.

Please refer to the .log in the output directory (second mandatory command line argument). Logfile contains the information about the number of reads detected in each step of the ROP pipeline.

An example of the .log

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ROP is a computational protocol aimed to discover the source of all reads, originated from complex RNA molecules, recombinant antibodies and microbial communities. Written by Serghei Mangul (smangul@ucla.edu) and Harry Taegyun Yang (harry2416@gmail.com), University of California, Los Angeles (UCLA). (c) 2016. Released under the terms of the General Public License version 3.0 (GPLv3)

For more details see:
http://serghei.bioinformatics.ucla.edu/rop/
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Processing 2505 unmapped reads
1. Quality Control...
--filtered 2193 low quality reads
--filtered 2 low complexity reads (e.g. ACACACAC...)
--filtered 22 rRNA reads
In toto : 2217 reads failed QC and are filtered out
2. Remaping to human references...
--identified 6 lost human reads from unmapped reads 
3. Mapping to repeat sequences...
-Identify 1 lost repeat sequences from unmapped reads
***Note : Repeat sequences classification into classes (e.g. LINE) and families (e.g. Alu) will be available in next release
3. Non-co-linear RNA profiling
Please use --circRNA options to profile circular RNAs
***Note : Trans-spicing and gene fusions  are currently not supported, but will be in the next release.
4a. B lymphocytes profiling...
--identified 0 reads mapped to immunoglobulin heavy (IGH) locus
--identified 0 reads mapped to immunoglobulin kappa (IGK) locus 
--identified 0 reads mapped to immunoglobulin lambda (IGL) locus
4b. T lymphocytes profiling...
--identified 0 reads mapped to T cell receptor alpha (TCRA) locus
--identified 0 reads mapped to T cell receptor beta (TCRB) locus
--identified 0 reads mapped to T cell receptor delta (TCRD) locus
--identified 0 reads mapped to T cell receptor gamma locus (TCRG) locus
In toto : 0 reads mapped to antibody repertoire loci
***Note : Combinatorial diversity of the antibody repertoire (recombinations of the of VJ gene segments)  will be available in the next release.
5.  Microbiome profiling...
--identified 0 reads mapped bacterial genomes
--identified 0 reads mapped viral genomes
--identified 4 reads mapped ameoba genomes
--identified 1 reads mapped crypto genomes
--identified 0 reads mapped giardia genomes
--identified 0 reads mapped microsporidia genomes
--identified 0 reads mapped piroplasma genomes
--identified 1 reads mapped plasmo genomes
--identified 1 reads mapped toxo genomes
--identified 0 reads mapped trich genomes
--identified 0 reads mapped tritryp genomes
In toto : 7 reads mapped to microbial genomes
Summary:   The ROP protocol is able to account for 2231 reads

Additionally ROP creates numberReads_<sampleName>.log with the number of reads detected in each step in the .csv format. An example of numberReads_<sampleName>.log is provided bellow:

sample,totalReads,lowQuality,lowComplexity,rRNA,lostHumanReads,lostRepeatReads,immuneReads,microbiomeReads,unaccountedReads
unmappedExample,2508,2193,2,22,6,1,5,7,272

ROP is also able to find the the source of mapped reads. ROP is able to categorize the mapped reads into genomic and repeat features. An example of a file with reads assigned to the genomic features is presented bellow:

SRR1146076.3540543,22,junction
SRR1146076.17070789,22,UTR5
SRR1146076.21758998,22,UTR5
SRR1146076.20543213,22,UTR5
SRR1146076.9808865,22,DEEP
SRR1146076.16863731,22,INTERGENIC
SRR1146076.968340,22,UTR3

Given ROP analysis for multiple sample, you may consider concatenate the individual logfiles to get the statistics across the multiple samples. Detail instructions are provided here