Hi All, I tried to submit paired end fastq files (R1 and R2) for a sample to NCBI SRA database. I tried the following steps:
1) Created a bioproject profile by following the link: https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB4422178/submitter Filled in everything and submitted to get SAMN and PRJNA ids, then I selected FTP uploads
2) Then went to https://submit.ncbi.nlm.nih.gov/subs/sra/ First I moved both R1 and R2 files to a separate directory and cd to that directory. Then in the terminal typed:
ftp -i open ftp-private.ncbi.nlm.nih.gov
Then on the prompt, typed username and password from link in 2
Username: subftp Password: w*******
cd to account folder from link in 2 cd firstname.lastname@example.org_00YmVxw2
3) Created a new directory as shown below:
mkdir rhizophagus cd rhizophagus
4) Then transfered both fastq files to ncbi directory by typing:
After transfer was complete, I typed
ls to see all files that have been transferred.
5) I then submitted the files using upload folder from https://submit.ncbi.nlm.nih.gov/subs/sra/ once the files were available on the database. I then selected the folder and submitted the folder.
Both of these files are now online here https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP158305. However, when I tried to download these file using
prefetch --option-file sratest.txt and extract with
fastq-dump --split-files SRP158305, I got two fastq files, but one file is 12.2 gb and the other file is only 303.3 mb. The actual file size of each fastq (R1 and R2) should be 10.9, but the downloaded fastq's are 12.2 gb and 303mb. I am not sure how it should have been submitted, but I would really if somebody could help me figure out where it went wrong. Thanks for your help in advance.