Translatome - ORFs detection - 《Bioinformatics》

模板

模板

Key parameters:
a. Start/Stop
b. Minimum ORF length
c. Reads filtering
d. Specific cutoff
0-base or 1-base
ORF type
Overlap in annotaion
Multiple start codons

Tools	Methods	Category	Key parameters	0-base or 1-base	ORF type	Multiple start codons
Ribotricer	Normalized projected vector	Frame pattern consistency	FDR filter: being set by phase-score cutoff (github or learning) —report_all (including result after FDR filtering). Cutoff of phase score can be learnt by command using RNA-seq and ribo-seq data.		Annotated uORF dORF overlap_uORF overlap_dORF novel super_uORF super_dORF
RiboCode	Wilcox single rank test	Frame preference	-p PVAL_CUTOFF (rule FDR filtering) filter: 0.05 (default}	1-base	annotated uORF dORF Overlap_dORF Overlap_uORF novel internal	The RiboCode generates two text files: The “(output file name).txt” contains the information of all predicted ORFs in each transcript. The “(output file name)_collapsed.txt” file combines the ORFs having the same stop codon in different transcript isoforms: the one harboring the most upstream in-frame ATG will be kept.
RiboTaper
ORFscore
RP-BP
ORF-RATER
RibORF
RiboWave
Ribo-TISH
RiboHMM
SaTAnn
PRICE (GEDI)
SPECtre
FLOSS

Tools	Input	Output	Identification level, file, column	ORF types	Offset,	Tips and FDR filter
Ribotricer	GTF Ref Bam2Ge (offset config)	1. Phase score 2. contain all 3. ORF type 4.T/G ID Tx_type 5.coor	(Exon) / Tx Result: ORF_pred.txt(Tx) Column: phase_score	Annotated uORF dORF overlap_uORF overlap_dORF novel super_uORF super_dORF	Automatically or manually	filter: being set by phase-score cutoff (github or learning) —report_all (including result after FDR filtering). Cutoff of phase score can be learnt by command using RNA-seq and ribo-seq data.
RiboCode	GTF Ref Bam2Tx (offset config)	1. pval_combined 2. not contain all 3. ORF type 4.T/G ID Tx_type 5.coor	(Exon) / Tx Result: ORF_pred.txt(Tx)/ ORF_pred.gtf(Ex)(给出了每个翻译的Tx的exon) Column: pval_combined (Exon level avaible in https://github.com/xryanglab/ORFcalling/tree/master/scripts/Figure2c)	annotated uORF dORF Overlap_dORF Overlap_uORF novel internal	Automatically or manually	-p PVAL_CUTOFF (rule FDR filtering) filter: 0.05 (default}
RiboTaper	GTF Ref RiboBam2Ge RNABam2Ge (offset config)	1. ORF_pval_multi_ribo 2. not contain all 3. ORF type 4.T/G ID Ex_type 5.coor	Exon/ Tx Result: ORFs_max Column: ORF_pval_multi_ribo FDR filter: 0.05	dORF lncRNA misc_RNA ORFs_ccds snRNA transcribed_unprocessed_pseudogene uORF	Manually	ORF_pval_multi_ribo, filter: 0.05(default) ORFs_max_filt (after filtering)
ORFscore	Contained in RiboTaper and Spectre	1. ORF_score, chi-square test 2. not contain all 3. ORF type 4.T/G ID Ex_type 5.coor	Exon/ Tx Result: Column: FDR filter:	NA	NA	NA
RibORF	GTF Ref RiboSam2Ge (offset config)	1. pred.pvalue 2. not contain all 3. ORF type 4.T/G ID type 5.coor	Tx Result: repre.valid.pred.pvalue.parameters.txt Column: pred.pvalue FDR filter: 0.05	canonical extension internal overlap.uORF polycistronic truncation uORF	Manually	-p predictPvalueCutoff FDR filter: 0.7(default)
ORF-RATER	GTF Ref	1. orfrating 2. not contain all 3. ORF type 4.T/G ID type 5.coor	Tx Result: quant.csv Column: orfrating FDR filter: 0.05	canonical extension internal overlap.uORF polycistronic truncation uORF	Automatically or manually	Orfratering: 0.3-1
RP-BP	Bam2Ge Configuration	1. bayes factor mean, 2. not contain all, 3. ORF type, 4.T/G ID type 5.coor	Tx Result: SRR5382424.alignments-only-unique.length-29-30.offset-12-12.frac-0.2.rw-0.bayes-factors.bed.gz Column: bayes factor mean FDR filter: 5	canonical canonical_variant five_prime five_prime_overlap noncoding overlap three_prime three_prime_overlap within	Manually	Option: min_bf_mean bf mean filter: 5 (default)
Ribowave	GTF Ref RiboSam2Ge (offset config)	1. pvalue, 2. contain all, 3. no ORF type, 4.T/G ID type 5.coor	Tx Result:SRR5382424.feats1 Column: pvalue FDR filter: 0.05	NA	Manually	Coor after (FDR:0.05) filtering in SRR5382424.95%.mx
RiboTISH	GTF Ref RiboSam2Ge (offset config)	1. RiboQvalue 2. contain all in pred_all.txt 3. ORF type 4.T/G ID type 5.coor	Tx Result: pred.txt/pred_all.txt Column: RiboQvaluve FDR filter: 0.05	:3’UTR 3’UTR:CDSFrameOverlap 3’UTR:Known 5’UTR 5’UTR:CDSFrameOverlap 5’UTR:Known Annotated Extended Extended:CDSFrameOverlap Extended:Known Internal Internal:CDSFrameOverlap Internal:Known Novel Novel:CDSFrameOverlap Novel:Known Truncated Truncated:Known	Manually	—allresult ALLRESULT —fsqth FSQTH qvalue FDR: 0.05 (default) type: https://github.com/zhpn1024/ribotish
RiboHMM	GTF Ref RiboSam2Ge (offset config)	1. RiboQvalue 2. contain all in pred_all.txt 3. ORF type 4.T/G ID type 5.coor	Tx Result: pred.txt/pred_all.txt Column: RiboQvaluve FDR filter: 0.05		Manually
Gedi(PRICE)	GTF Ref RiboSam2Ge	1. p value 2. contain all in SRR5382424.orfs.tsv 3. ORF type 4.T/G ID type 5.coor	Tx Result: SRR5382424.orfs.tsv Column: p value FDR filter: 0.1	CDS dORF iORF ncRNA orphan Trunc uoORF uORF Variant (Ext, intronic)	Automatically	-fdr : 10% (default) p value type: https://github.com/erhard-lab/gedi/wiki/Price#output-files
Spectre	GTF Ref RiboSam2Ge Cufflinks (offset config)	1. spectre_score 2. not contain all(full?) 3. ORF type 4.T/G ID type 5.coor	Tx Result: spectre.txt Column: spectre_score FDR filter: 0.05	3’UTR 5’UTR CDS	Manually	—fdr 0.05 (default)
SaTAnn	GTF Ref RiboSam2Ge (offset config)	1. pval_uniq 2. not contain all 3. ORF type 4.T/G ID type 5.coor	Tx Result: bam_for_SaTAnn_final_SaTAnn_results Column: SaTAnn_results$ORFs_tx$pval_uniq FDR filter: 0.05	“ORF_annotated” “N_truncation” “overl_dORF” “novel” “uORF” “nested_ORF” “dORF” “N_extension” “overl_uORF” “C_extension” “C_truncation”	Manually	pval_uniq<0.05 in result