RNAmod | Analysis

Modification calling and annotations

Upload your meRIP-seq data to call and annotation modifications:

Input file is in FASTQ file.
To speed the uploading, we require the users to compress the file into .zip or .gz format.

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 *

FASTQ

Upload sequencing data

Layout *

Single-end Paired-end

Input *

Human (.fq.gz)

IP *

Human (.fq.gz)

Input *

Paired-end 1 (.fastq, .fq, .zip, .gz)

Paired-end 2 (.fastq, .fq, .zip, .gz)

IP *

Paired-end 1 (.fastq, .fq, .zip, .gz)

Paired-end 2 (.fastq, .fq, .zip, .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 select or input the adapter

Max. error rate

Min. adapter fragment Length

Remove 5' nucleotides

Remove 3' nucleotides

Minimum read length

Phred quality score

Adapter Trimming *

Please select or input the adapter for paired-end #1

Please select or input the adapter for paired-end #2

Max. error rate

Min. adapter fragment Length

Remove 5' nucleotides for P1

Remove 3' nucleotides for P1

Remove 5' nucleotides for P2

Remove 3' nucleotides for P2

Minimum read length

Phred quality score

Sample names *

Not space character in the name

Parameters for modification calling

Allowed mismatch in read mapping *

Mismatch 0-3

Max. of multiple-mapping *

Multiple mapping times

Tool *

MACS2 ExomePeak2

extsize *

The arbitrary extension size in bp

nomodel *

Whether or not to build the shifting model

Fragment length *

Fragment length in bp

Binding length *

Binding length in bp

Peak calling mode *

Peak calling mode

Fragment length *

Fragment length in bp

Window width *

Window width

Fold enrichment *

Fold enrichment

P-value *

FDR (q-value) cutoff for peak detection

Q-value *

FDR (q-value) cutoff for peak detection

Parameters for modification annotations

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

Genes for GO analysis

All genes with modifications Upload gene background

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

GTF files

Select the reference genome and input type

Upload sequencing data

Parameters for modification calling

Parameters for modification annotations