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 here to check the 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.
FASTQ format
The raw data file can be in FASTQ format (See the figure below as example)
To further minimize the size of uploading file, users are highly recommended to use gzip (for Linux and Mac OS) to compress the fasta file into gz format file or use winrar (for Windows) to compress the fasta file into zip format file.
GTF files
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 |
Cucumis sativus chineseLong v3 | Chinese Long v3 | Cucurbitgenomics | 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 |