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FLARE: a fast and flexible workflow for identifying RNA editing foci.

Eric Kofman, Brian Yee, Hugo C Medina-Munoz, Gene W Yeo
BMC bioinformatics · 2023 · Vol. 24 (1) · pp. 370
PubMed DOI PMC Full Text

Abstract

Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable to false positives due to off-target editing, genetic variation and sequencing errors. We present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the outputs of the SAILOR edit site discovery tool to identify regions statistically enriched for RNA editing. FLARE can be configured to analyze any type of RNA editing, including C to U and A to I. We applied FLARE to C-to-U editing data from a RBFOX2-APOBEC1 STAMP experiment, to show that our approach attains high specificity for detecting RBFOX2 binding sites. We also applied FLARE to detect regions of exogenously introduced as well as endogenous A-to-I editing. FLARE is a fast and flexible workflow that identifies significantly edited regions from RNA-seq data. The FLARE codebase is available at https://github.com/YeoLab/FLARE .

Publication Types

["Journal Article"]

Keywords

["Clustering", "Modeling", "RNA editing", "Statistical"]

MeSH Terms

["RNA Editing", "Workflow", "RNA", "RNA-Seq", "Binding Sites", "APOBEC-1 Deaminase"]

Funding

U24 HG009889 NHGRI NIH HHS (United States)
R01 HG004659 NHGRI NIH HHS (United States)
RF1 MH126719 NIMH NIH HHS (United States)
R01 HG011864 NHGRI NIH HHS (United States)
T32 CA067754 NCI NIH HHS (United States)
U41 HG009889 NHGRI NIH HHS (United States)
K12 GM068524 NIGMS NIH HHS (United States)
K12-GM068524 NIH HHS (United States)
RF1-MH126719 NIH HHS (United States)
R01-HG004659 NHGRI NIH HHS (United States)
R01-HG011864 NHGRI NIH HHS (United States)
U41/U24-HG009889 NHGRI NIH HHS (United States)

Linked Datasets (8)

GSE166402 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

Homo sapiens
9 data files
FileTypeSize
NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB
NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB
NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB
NTIA_2_S2_L001_R1_001.fastq.gz RIP-Seq 333.4 MB
PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB
PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB
PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB
PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB
SRR13663712.lite RIP-Seq 333.4 MB
GSE155729 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Homo sapiens
GSE215252 GSE via ncbi_elink
GEO

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Homo sapiens
3 data files
FileTypeSize
RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted.STAR… RNA-Seq 145.6 MB
RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted.STAR… RNA-Seq 142.8 MB
RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted.STAR… RNA-Seq 98.0 MB
GSE155649 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

Homo sapiens
77 data files
FileTypeSize
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Apobec_plusT_2_S31_L003_R1_001.fastq.gz OTHER 631.7 MB
Apobec-T_1_S28_L003_R1_001.fastq.gz OTHER 614.7 MB
Apobec-T_2_S29_L003_R1_001.fastq.gz OTHER 814.8 MB
ApoControl-0_S7_L001_R1_001.fastq.gz OTHER 1.5 GB
ApoControl-1000_S21_L002_R1_001.fastq.gz OTHER 1.5 GB
ApoControl-50_S14_L002_R1_001.fastq.gz OTHER 1.3 GB
RBFOX2-0_S6_L001_R1_001.fastq.gz OTHER 1.4 GB
RBFOX2-1000_S20_L002_R1_001.fastq.gz OTHER 1.6 GB
RBFOX2-50_S13_L002_R1_001.fastq.gz OTHER 1.4 GB
RPS2-0_S4_L001_R1_001.fastq.gz OTHER 1.1 GB
RPS2-1000_S18_L002_R1_001.fastq.gz OTHER 1.4 GB
RPS2-50_S11_L001_R1_001.fastq.gz OTHER 1.5 GB
RPS3-0_S5_L001_R1_001.fastq.gz OTHER 1.8 GB
RPS3-1000_S19_L002_R1_001.fastq.gz OTHER 1.8 GB
Sample_10_S60_L006_R1_001.fastq.gz OTHER 925.3 MB
Sample11_S29_merged.fastq.gz OTHER 133.9 MB
Sample12_S30_merged.fastq.gz OTHER 131.5 MB
Sample13_S31_merged.fastq.gz OTHER 148.9 MB
Sample14_S13_merged.fastq.gz OTHER 457.9 MB
Sample15_S14_merged.fastq.gz OTHER 349.1 MB
Sample16_S32_merged.fastq.gz OTHER 92.0 MB
Sample17_S15_merged.fastq.gz OTHER 357.1 MB
Sample18_S16_merged.fastq.gz OTHER 271.3 MB
Sample19_S17_merged.fastq.gz OTHER 422.5 MB
Sample1_S23_merged.fastq.gz OTHER 225.8 MB
Sample20_S18_merged.fastq.gz OTHER 302.1 MB
Sample21_S33_merged.fastq.gz OTHER 154.6 MB
Sample22_S34_merged.fastq.gz OTHER 125.2 MB
Sample23_S35_merged.fastq.gz OTHER 260.5 MB
Sample24_S36_merged.fastq.gz OTHER 132.1 MB
Sample25_S19_merged.fastq.gz OTHER 273.1 MB
Sample26_S20_merged.fastq.gz OTHER 241.7 MB
Sample27_S37_merged.fastq.gz OTHER 146.2 MB
Sample28_S21_merged.fastq.gz OTHER 344.7 MB
Sample29_S38_merged.fastq.gz OTHER 265.3 MB
Sample2_S24_merged.fastq.gz OTHER 172.2 MB
Sample30_S39_merged.fastq.gz OTHER 138.2 MB
Sample31_S40_merged.fastq.gz OTHER 139.6 MB
Sample32_S22_merged.fastq.gz OTHER 237.7 MB
Sample_33_S61_L006_R1_001.fastq.gz OTHER 440.1 MB
Sample_34_S62_L006_R1_001.fastq.gz OTHER 556.8 MB
Sample_35_S63_L006_R1_001.fastq.gz OTHER 882.0 MB
Sample_36_S64_L006_R1_001.fastq.gz OTHER 538.0 MB
Sample_37_S65_L006_R1_001.fastq.gz OTHER 664.4 MB
Sample_38_S66_L006_R1_001.fastq.gz OTHER 963.6 MB
Sample_39_S67_L006_R1_001.fastq.gz OTHER 715.0 MB
Sample_3_S57_L006_R1_001.fastq.gz OTHER 980.1 MB
Sample_40_S68_L006_R1_001.fastq.gz OTHER 730.7 MB
Sample41_S41_merged.fastq.gz OTHER 63.0 MB
Sample42_S42_merged.fastq.gz OTHER 124.1 MB
Sample4_S25_merged.fastq.gz OTHER 211.6 MB
Sample5_S26_merged.fastq.gz OTHER 205.2 MB
Sample_6_S58_L006_R1_001.fastq.gz OTHER 587.0 MB
Sample7_S27_merged.fastq.gz OTHER 209.6 MB
Sample8_S28_merged.fastq.gz OTHER 226.2 MB
Sample_9_S59_L006_R1_001.fastq.gz OTHER 720.2 MB
SLBP_0_48hr_A_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_48hr_B_merged_R1.fastq.gz OTHER 1.5 GB
SLBP_0_48hr_C_merged_R1.fastq.gz OTHER 1.7 GB
SLBP_0_72hr_A_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_72hr_B_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_72hr_C_merged_R1.fastq.gz OTHER 1.1 GB
SLBP_1000_72hr_A_merged_R1.fastq.gz OTHER 937.1 MB
SLBP_1000_72hr_B_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_1000_72hr_C_merged_R1.fastq.gz OTHER 1.1 GB
TI_55_S13_L001_R1_001.fastq.gz OTHER 883.8 MB
TI_56_S14_L001_R1_001.fastq.gz OTHER 241.8 MB
TI_58_S15_L001_R1_001.fastq.gz OTHER 262.8 MB
TI_59_S16_L001_R1_001.fastq.gz OTHER 718.1 MB
TI_8_S6_L001_R1_001.fastq.gz RNA-Seq 958.8 MB
Tia1_0ng_1_S40_L003_R1_001.fastq.gz OTHER 951.1 MB
Tia1_0ng_2_S41_L003_R1_001.fastq.gz OTHER 708.4 MB
Tia1_1000ng_1_S14_L001_R1_001.fastq.gz OTHER 486.1 MB
Tia1_1000ng_2_S27_L002_R1_001.fastq.gz OTHER 581.7 MB
Tia1_50ng_1_S42_L003_R1_001.fastq.gz OTHER 722.9 MB
Tia1_50ng_2_S13_L001_R1_001.fastq.gz OTHER 792.6 MB
GSE155708 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Homo sapiens
6 data files
FileTypeSize
APOBEC_cDNA_all_pass.fastq.gz RNA-Seq 7.7 GB
APOBEC_dRNA.fastq.gz RNA-Seq 545.2 MB
RBFOX2_cDNA_all_pass.fastq.gz RNA-Seq 21.1 GB
RBFOX2_dRNA.fastq.gz RNA-Seq 1.2 GB
SRR12389274 RNA-Seq 7.7 GB
SRR12389276.lite RNA-Seq 21.1 GB
GSE155726 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Homo sapiens
5 data files
FileTypeSize
control_STAMP_possorted_genome_bam.bam RNA-Seq 12.0 GB
NPC_HEK_control_STAMP_possorted_genome_bam.bam RNA-Seq 8.6 GB
NPC_HEK_RBFOX2_STAMP_possorted_genome_bam.bam RNA-Seq 8.6 GB
RBP_STAMP_possorted_genome_bam.bam RNA-Seq 18.6 GB
RPS2_STAMP_possorted_genome_bam.bam RNA-Seq 12.3 GB
GSE155728 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Homo sapiens
3 data files
FileTypeSize
TIA_293T.rep1_clip.r1.reformatted.fq.gz RIP-Seq 291.5 MB
TIA_293T.rep1_input.NIL.r1.fq.gz RIP-Seq 460.5 MB
TIA_293T.rep2_clip.r1.reformatted.fq.gz RIP-Seq 178.8 MB
GSE166404 GSE via ncbi_elink
GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Homo sapiens
30 data files
FileTypeSize
CCS_Demux_5759_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 32.0 MB
CCS_Demux_5759_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 29.7 MB
CCS_Demux_5759_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 20.7 MB
CCS_Demux_5759_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 12.6 MB
CCS_Demux_5759_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 19.5 MB
CCS_Demux_5759_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 28.2 MB
CCS_Demux_5779_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 327.6 MB
CCS_Demux_5779_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 291.7 MB
CCS_Demux_5779_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 228.5 MB
CCS_Demux_5779_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 141.2 MB
CCS_Demux_5779_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 208.6 MB
CCS_Demux_5779_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 293.3 MB
CCS_Demux_5896_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 52.7 MB
CCS_Demux_5896_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 63.0 MB
CCS_Demux_5896_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 46.5 MB
CCS_Demux_5896_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 39.6 MB
CCS_Demux_5896_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 55.5 MB
CCS_Demux_5896_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 60.4 MB
CCS_Demux_6465_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 37.6 MB
CCS_Demux_6465_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 55.7 MB
CCS_Demux_6465_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 37.0 MB
CCS_Demux_6465_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 38.8 MB
CCS_Demux_6465_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 49.2 MB
CCS_Demux_6465_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 52.9 MB
CCS_Demux_6499_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 43.8 MB
CCS_Demux_6499_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 34.3 MB
CCS_Demux_6499_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 28.8 MB
CCS_Demux_6499_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 17.3 MB
CCS_Demux_6499_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 27.2 MB
CCS_Demux_6499_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 39.1 MB

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