RiboToolkit | Analysis

Single case analysis

Upload your Ribo-seq data to comprehensively study RNA translation:

Input file could be in collapsed FASTA format ( How to prepare the FASTA inputs) , accessible web link to the FASTA file, and FASTQ file.
To speed the uploading, we highly recommend the users to compress the file into .zip or .gz format
Refer this table and this site to check the reference genome and annotation GTF files used for each species.
The users can check the RPF metagene plot around translation start sites in the result page for P-site inferring manually and re-run the analysis using "User define" option.

SN	Species	Genome version	Source	Class
1	Homo sapiens	hg19	GENCODE	Animal
2	Homo sapiens	hg38.gencode_v46	GENCODE	Animal
3	Homo sapiens	hg38	GENCODE	Animal
4	Mus musculus	mm10	GENCODE	Animal
5	Mus musculus	mm39	GENCODE	Animal
6	Rattus norvegicus	rn6	Ensembl	Animal
7	Danio rerio	dre_GRCz11	Ensembl	Animal
8	Bos taurus	bta.ARS-UCD1.2	Ensembl	Animal
9	Canis lupus familiaris	clu.ROS_Cfam_1.0	Ensembl	Animal
10	Gallus gallus	gga.GRCg7b	Ensembl	Animal
11	Gorilla gorilla	ggo.gorGor4	Ensembl	Animal
12	Macaca mulatta	mml.Mmul_10	Ensembl	Animal
13	Pan troglodytes	ptr.Pan_tro_3.0	Ensembl	Animal
14	Sus scrofa	ssc.Sscrofa11.1	Ensembl	Animal
15	Xenopus tropicalis	xtr.UCB_Xtro_10.0	Ensembl	Animal
16	Caenorhabditis elegans	cel_WBcel235	Ensembl	Animal
17	Drosophila melanogaster	dme_BDGP6	Ensembl	Insect
18	Anopheles gambiae	aga.AgamP4	Ensembl	Insect
19	Locusta migratoria	lmi.240118	Other	Insect
20	Saccharomyces cerevisiae	sce_R64	Ensembl	Fungus
21	Neurospora crassa	ncr.NC12	Ensembl	Fungus
22	Arabidopsis thaliana	ara_TAIR10	Ensembl	Plant
23	Acer truncatum	atr.v1	Ensembl	Plant
24	Adiantum capillus-veneris	aca.ASM1452938v2	Ensembl	Plant
25	Amphidinium carterae	aca.v2	Ensembl	Plant
26	Brassica napus	bna.AST_PRJEB5043_v1	Ensembl	Plant
27	Brassica rapa	bra.Brapa_1.0	Ensembl	Plant
28	Brachypodium distachyon	bdi.v3.0	Ensembl	Plant
29	Camellia sinensis	csi.AHAU_CSS_1	Ensembl	Plant
30	Chlamydomonas reinhardtii	cre.v5.5	Ensembl	Plant
31	Cucumis sativus chineseLong v3	csa_chineseLong_v3	Ensembl	Plant
32	Cucumis sativus	csa.ASM407v2	Ensembl	Plant
33	Dalbergia cultrat	dcug.v1	Ensembl	Plant
34	Glycine max	gma_v2	Ensembl	Plant
35	Gossypium raimondii	gra.Graimondii2_0_v6	Ensembl	Plant
36	Hordeum vulgare	hvu.MorexV3	Ensembl	Plant
37	Litchi chinensis	lch.v1	Ensembl	Plant
38	Malus domestica golden	mdo.ASM211411v1	Ensembl	Plant
39	Medicago truncatula	mtr.MedtrA17_4.0	Ensembl	Plant
40	Nicotiana benthamiana	nbe.v1	Ensembl	Plant
41	Nicotiana tabacum	ntab.TN90	Ensembl	Plant
42	Oryza sativa	osa_IRGSP_1	Ensembl	Plant
43	Oryza sativa	osa_msu7	Other	Plant
44	Oryza sativa	osa_huazhan	Other	Plant
45	Oryza sativa	Basmati1.IGDBv1	Pan_rice_33	Plant
46	Oryza sativa	CG14.IGDBv1	Pan_rice_33	Plant
47	Oryza sativa	G46.IGDBv1	Pan_rice_33	Plant
48	Oryza sativa	IR64.IGDBv1	Pan_rice_33	Plant
49	Oryza sativa	Lemont.IGDBv1	Pan_rice_33	Plant
50	Oryza sativa	LJ.IGDBv1	Pan_rice_33	Plant
51	Oryza sativa	MSU.IGDBv1	Pan_rice_33	Plant
52	Oryza sativa	NamRoo.IGDBv1	Pan_rice_33	Plant
53	Oryza sativa	N22.IGDBv1	Pan_rice_33	Plant
54	Oryza sativa	TM.IGDBv1	Pan_rice_33	Plant
55	Oryza sativa	Tumba.IGDBv1	Pan_rice_33	Plant
56	Oryza sativa	WSSM.IGDBv1	Pan_rice_33	Plant
57	Oryza rufipogon	oru.OR_W1943	Ensembl	Plant
58	Oryza indica	osai.ASM465v1	Ensembl	Plant
59	Populus trichocarpa	ptc.Pop_tri_v3	Ensembl	Plant
60	Physcomitrium patens	ppa.Phypa_V3	Ensembl	Plant
61	Selaginella moellendorffii	smo.v1	Ensembl	Plant
62	Solanum lycopersicum	sly_SL3	Ensembl	Plant
63	Solanum tuberosum	stu.SolTub_3.0	Ensembl	Plant
64	Sorghum bicolor	sbi.NCBIv3	Ensembl	Plant
65	Symbiodinium kawagutii	ska.Fugka2468_1	Ensembl	Plant
66	Triticum aestivum	tae.IWGSC	Ensembl	Plant
67	Vitis vinifera	vvi.PN40024.v4	Ensembl	Plant
68	Zea mays	zma_RefGen_v4	Ensembl	Plant
69	Zea mays	zma.B73_NAM5.0	Ensembl	Plant
70	Escherichia coli	ecoli_k12	Ensembl	Bacteria
71	Bacillus subtilis	bsu_168	Ensembl	Bacteria
72	Pyrococcus furiosus	pfu_dsm_3638	Ensembl	Bacteria
73	Halobacterium salinarum	hsa_NRC1	Ensembl	Bacteria
74	Methanosarcina mazei	mma.ASM706v1	Ensembl	Bacteria
75	Acetobacterium woodii	awo_gca_000247605	Ensembl	Bacteria
76	Bacteroides thetaiotaomicron	bth_gca_000011065	Ensembl	Bacteria
77	Caulobacter vibrioides	cvi_gca_000022005	Ensembl	Bacteria
78	Clostridium aceticum	cac_gca_001042715	Ensembl	Bacteria
79	Clostridium drakei	cdr_gca_003096175	Ensembl	Bacteria
80	Clostridium ljungdahlii	clj_gca_000143685	Ensembl	Bacteria
81	Escherichia coli	eco_gca_000931565	Ensembl	Bacteria
82	Eubacterium limosum	eli_gca_001481725	Ensembl	Bacteria
83	Flavobacterium johnsoniae	fjo_gca_000016645	Ensembl	Bacteria
84	Halobacterium salinarum	hsa_gca_000006805	Ensembl	Bacteria
85	Haloferax volcanii	hvo_gca_000025685	Ensembl	Bacteria
86	Klebsiella michiganensis	kmi_gca_000963575	Ensembl	Bacteria
87	Lacticaseibacillus rhamnosusGG	lrh_gca_002287945	Ensembl	Bacteria
88	Listeria innocua	lin_gca_000195795	Ensembl	Bacteria
89	Listeria monocytogenes	lmo_gca_000196035	Ensembl	Bacteria
90	Mycobacterium tuberculosis	mtu_gca_000016145	Ensembl	Bacteria
91	Mycobacteroides abscessus	mab_gca_000069185	Ensembl	Bacteria
92	Mycolicibacterium smegmatis	msm_gca_000015005	Ensembl	Bacteria
93	Pseudomonas aeruginosa	pae_gca_002968755	Ensembl	Bacteria
94	Pseudomonas fluorescens	pfl_gca_001307155	Ensembl	Bacteria
95	Salmonella enterica	sen_gca_003325055	Ensembl	Bacteria
96	Sinorhizobium meliloti	sme_gca_002197125	Ensembl	Bacteria
97	Staphylococcus aureus	sau_gca_001018655	Ensembl	Bacteria
98	Streptococcus pneumoniae	spn_gca_000018965	Ensembl	Bacteria
99	Streptomyces avermitilis	sav_gca_000009765	Ensembl	Bacteria
100	Streptomyces clavuligerus	scl_GCF_005519465	Ensembl	Bacteria
101	Streptomyces coelicolor	sco_GCF_000203835	Ensembl	Bacteria
102	Streptomyces griseus	sgr_gca_000010605	Ensembl	Bacteria
103	Streptomyces lividans	sli_GCF_000739105	Ensembl	Bacteria
104	Streptomyces tsukubensis	sts_GCF_003932715	Ensembl	Bacteria
105	Streptomyces venezuelae	sve_gca_000253235	Ensembl	Bacteria
106	Synechocystis sp.	syn_gca_000478825	Ensembl	Bacteria
107	Vibrio natriegens	vna_gca_001680085	Ensembl	Bacteria
108	Vibrio vulnificus	vvu_gca_000039765	Ensembl	Bacteria
109	Zymomonas mobilis	zmo_gca_000007105	Ensembl	Bacteria

The fields marked by "*" are required!

Select the reference genome and input type

Species *

Please choose a species for the analysis

Input type *

Collapsed FASTA Links to FASTA FASTQ Reanalysis

Upload Ribo-seq sequences

Sample1 *

Mouse Human (.fa, .fa.zip, .fa.gz) Mouse (.fq.gz)

Links *

Provide links to download your collapsed FASTA data (Example)

Job ID(s) *

Provide completed job ID(s) to re-analyze your data with different parameters

Adapter Trimming *

Please choose the 3'adapter or input the adapter (mandatory)

Please choose or input the 5' adapter (optional)

Max. error rate

Min. adapter fragment Length

Remove 5' nucleotides

Remove 3' nucleotides

Round of adapter trimming

Phred quality score

Parameters for RPF analysis

Sample names *

Separate multiple sample names by comma ","

RPF length of interval (nt) *

Shortest RPF Length Longest RPF Length

Allowed mismatch in RPF mapping *

Mismatch 0-3

Max. of multiple-mapping *

Multiple mapping times

Remove duplicates

Not remove Remove

Length of UMI sequence (bp)

UMI location

Offsets to infer P-sites

Calculate by RiboToolkit User define

RPF lengths and offsets (separated by blank)

Min. coverage for pause sites *

Coverage cutoff for codon pause sites

Min. coverage for pause sites *

Coverage cutoff for codon pause sites

Exclude RPFs from
traslation start sites *

Number of codons

Fold change for pause sites *

Fold change of coverage between pauses and background

ORF p-value *

P-value cutoff for active translated ORFs

Get an notification when the job is done (optional)

FASTQ format

GTF files

Select the reference genome and input type

Upload Ribo-seq sequences

Parameters for RPF analysis