If you want to publish results on short reads you have to publish your data.
- For genomic data you can submit it in the Short Read Archive (SRA).
- For RNAseq data you can submit it in MAGE-TAG: http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi.
Please follow the instructions here
with a SRA run id (eg SRR1045854) type :
create ncbi directory:
create link :
ln -s ~/work/ncbi ~/ncbi
donwload data :
prefetch SRR1045854Your data will be available ~/wor/ncbi/public/sra/SRR1045854.sra
convert sra to fastq
After conversion, remove .sra file to save disk space.
You should use file from ENA as the protocol is much much much faster and files are already in fastq format.
- Find your dataset at https://www.ebi.ac.uk/ena/. Here is an example
Find the FASTQ url in columns "FASTQ files (FTP)", in the example it's :
On Genotoul cluster type :
ascpwrap.pl ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR104/003/SRR1045853/SRR1045853.fastq.gz .