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Figure 3 | BMC Genomics

Figure 3

From: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

Figure 3

Validation of putative chimeric RNAs. A) Relation between levels of expression and number of chimeras. The graph represents the number of chimeric reads per gene versus gene expression levels for M. pneumoniae (in black) and P. aeruginosa (in red). Sample obtained after mixing RNA of M. pneumoniae and P. aeruginosa in a ratio 1:1. B) Representation of putative chimeric RNAs in M. pneumoniae after validation filters. Black dots represent the 43.399 initial candidates. Grey dots, putative chimeric RNAs after filtering by Ωse and Ωpe scores (4047). Pink dots, candidates after applying staircase filter (74). Dark red dots,the putative chimerias obtained after applying the unique reads filter (33). C) Representation of a “box-pattern” profile of the reads corresponding to a M. pneumoniae chimeria comprising two regions of the rRNA. Grey arrow represents the genomic regions of M. pneumoniae and blue and black arrows, the junction positions in the pileup of the sequenced reads. D) Representation of reads for an artificial chimeric RNA result of ligation of tRNA of M. pneumoniae and rRNA of P. areuginosa. Arrows represent the genomic regions of M. pneumoniae (in grey) and P. aeruginosa (in dark red). Blue and black arrows indicate the positions of the junction in the genome and in the pileup of the sequenced reads. E) Staircase profile can be observed for the different reads that cover the junction of the chimeric RNA in P. aeruginosa. Dark red arrow represents the genome region that codes for the RNA. Blue and black arrows indicate the positions of the junction in the genome. F) Representation of reads for a putative chimeric RNA in M. pneumoniae. Grey arrow represents the genome region that codes for the RNA. Blue and black arrows, the junction positions in the pileup of sequenced reads.

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