# UPLOAD REFERENCES

<span style="font-weight: 400;">The latest versions of reference genomes and transcriptomes are available on the platform for eight model organisms. Pre-configured references can be explored through </span>**REFERENCES** <span style="font-weight: 400;">(Fig.). The</span>*<span style="font-weight: 400;"> owner</span>*<span style="font-weight: 400;"> column helps to identify the pre-configured references (owned by Stanome) from the custom references (owned by the users).</span>

<span style="font-weight: 400;">Click the </span>**REFERENCES**<span style="font-weight: 400;"> tab on the </span>**Upload**<span style="font-weight: 400;"> window to upload genome and transcriptome files.</span>

![Fig. 1. REFERENCE FILES upload window. Fields shown in red are mandatory.](https://docs.stanome.com/uploads/images/gallery/2022-01/embedded-image-azuy5jy3.png)

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Complete all the fields in the form before selecting the files.</span>

1. <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Add to Existing: </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Helps to add additional files such as transcriptome/genome. to an existing genome/transcriptome. This is an optional parameter (Default: No). </span>
2. <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Organism\*:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> Select the organism name.</span>
3. <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">Version\*:</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> Provide </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: italic; font-variant: normal; white-space: pre-wrap;">Genome</span> <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: italic; font-variant: normal; white-space: pre-wrap;">Build</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> (version) name or the number of the reference file(s). This will help to select the correct reference version during analysis.</span>

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #091e42; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"><span style="border-width: initial; border-style: none; display: inline-block; overflow: hidden; width: 20px; height: 25px;">![](https://lh5.googleusercontent.com/jqY7qNWYSe2lHp7E43C59wY0dLDXa-bk4cJq0vqjzGHCsebb1hOz9KAd_QFgb_8SvqSAUevHRnSIRTUxCgOGPcubVbXSMEXaRR7pioTMrnIyyFZ1xvwVpu4LOy5_AD8sHcRlMftZ)</span></span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #091e42; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">HINT</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #091e42; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> - </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Allowed formats for genome or transcriptome files are fa, fasta, fna, and their compressed formats. Each file should be compressed separately.</span>

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Following actions are performed on the uploaded references:</span>

- <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Uncompression of the files</span>
- <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Validation of the format and integrity of the file</span>
- <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Registration into the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">REFERENCES</span>
- <span style="font-size: 12pt; font-family: Montserrat, sans-serif; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Status notification through email</span>

<span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">Successfully uploaded reference files are stored in the </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #38761d; background-color: transparent; font-weight: bold; font-style: normal; font-variant: normal; white-space: pre-wrap;">REFERENCES</span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;">. Custom references can be deleted using </span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"><span style="border-width: initial; border-style: none; display: inline-block; overflow: hidden; width: 21px; height: 23px;">![](https://lh4.googleusercontent.com/Lvjj7mbMRobt0C7pZ_GsUxc1loo_mowP0s3iAFDfOHczLSb1pCeDlsHL0MdHoRKrzxf5qQJFsZN552NLmMJOUEn6dZFvit-lNMpvzkeD4SYB6gAKbvTajer2qHNYlELpL7-MqD4l)</span></span><span style="font-size: 12pt; font-family: Montserrat, sans-serif; color: #232a3c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; white-space: pre-wrap;"> on the reference details window.</span>