RNAmod | Analysis

Different modification model analysis

Upload your RNA modification sites:

Input file could be in BED format , accessible web link to the BED file.
To speed the uploading, we highly recommend the users to compress the file into .zip or .gz format
Refer here to check the GTF files used for each species.

Species	Genome version	Source	Download
Homo sapien	hg19	GENCODE	gtf file
Homo sapien	hg38	GENCODE	gtf file
Mus musculus	mm10	GENCODE	gtf file
Mus musculus	mm39	GENCODE	gtf file
Rattus norvegicus	rn6	Ensembl	gtf file
Danio rerio	GRCz11	Ensembl	gtf file
Bos taurus	ARS-UCD1.2	Ensembl	gtf file
Canis lupus familiaris	ROS Cfam 1.0	Ensembl	gtf file
Gallus gallus	GRCg7b	Ensembl	gtf file
Gorilla gorilla	gorGor4	Ensembl	gtf file
Macaca mulatta	Mmul_10	Ensembl	gtf file
Pan troglodytes	Pan_tro_3.0	Ensembl	gtf file
Sus scrofa	Sscrofa11.1	Ensembl	gtf file
Xenopus tropicalis	UCB Xtro 10.0	Ensembl	gtf file
Drosophila melanogaster	Dm6	Ensembl	gtf file
Caenorhabditis elegans	WBcel235	Ensembl	gtf file
Saccharomyces cerevisiae	R64	Ensembl	gtf file
Anopheles gambiae	AgamP4	Ensembl	gtf file
Arabidopsis thaliana	TAIR10	Ensembl	gtf file
Oryza sativa	IRGSP-1.0	Ensembl	gtf file
Zea mays	B73_RefGen_v4	Ensembl	gtf file
Zea mays	B73 NAM 5.0	Ensembl	gtf file
Glycine max	Wm82.a2/gma_v2	Ensembl	gtf file
Solanum lycopersicum	SL3.0	Ensembl	gtf file
Vitis vinifera	PN40024.v4	Ensembl	gtf file
Triticum aestivum	IWGSC RefSeq 1.0	Ensembl	gtf file
Sorghum bicolor	NCBIv3	Ensembl	gtf file
Solanum tuberosum	SolTub 3.0	Ensembl	gtf file
Populus trichocarpa	Pop_tri_v3	Ensembl	gtf file
Physcomitrium patens	Phypa_V3	Ensembl	gtf file
Medicago truncatula	MedtrA17 4.0	Ensembl	gtf file
Gossypium raimondii	Graimondii2_0_v6	Ensembl	gtf file
Cucumis sativus	ASM407v2	Ensembl	gtf file
Chlamydomonas reinhardtii	v5.5	Ensembl	gtf file
Brassica rapa	Brapa 1.0	Ensembl	gtf file
Brachypodium distachyon	bdi.v3.0	Ensembl	gtf file
Malus domestica golden	ASM211411v1	Ensembl	gtf file
Escherichia coli	K-12 MG1655	Ensembl	gtf file
Bacillus subtilis	Strain 168	Ensembl	gtf file
Pyrococcus furiosus	DSM 3638	Ensembl	gtf file
Halobacterium salinarum	NRC1	Ensembl	gtf file

The fields marked by "*" are required!

Select the reference genome and input type

Species *

Please choose a species for the analysis

Input type *

BED file Links to BED file Reanalysis

Upload modification data

Sample1 *

Mouse Human (.bed, .bed.zip, .bed.gz)

Links *

Provide links to download your motification site data (Example)

job ID(s) *

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

Sample names *

Separate names by comma ","

Parameters for modification site annotation

Flank size (bp) *

Flank size for transcription start/end sites (genomic level) Flank size for translation start/end sites and splice sites (transcript level)

Number of bins *

Divide gene feature into equal bins (features with length small than this value are excluded)

Scale RNA feature *

Scale the length of CDS and UTR in mRNA metagene plot

Please input gene symbols or Ensembl Gene IDs Example (hsa)

Motif parameters *

Motif width (separated by comma for multiple widths, such as 6,7,8 and 5,6)

Use subset of modification sites (score information are required in BED6)

Get an notification when the job is done (optional)

FASTQ format

BED format

GTF files

Select the reference genome and input type

Upload modification data

Parameters for modification site annotation