Better use prefetch or fastq-dump download, instead of wget !
Many .sra files are compressed against a reference which is not included in the .sra file. The SRA-tools prefetch or fastq-dump automatically download both the .sra files and the reference sequences required for decompressing. Additionally it gives download success control.
srapath SRR649944 http://sra-download.ncbi.nlm.nih.gov/srapub/SRR649944 wget -P Data http://sra-download.ncbi.nlm.nih.gov/srapub/SRR649944 ls Data/ SRR649944 fastq-dump --split-3 Data/SRR649944 ls SRR649944_1.fastq SRR649944_2.fastq many samples will not work using wget, as the compression related reference genome is missing Solution: use prefetch or fastq-dump, instead of wget fastq-dump --split-3 SRR649944 (only access number without path Data/SRR649944 or ./SRR649944) will force fastq-dump to download the sample directly from NCBI instead of using the local copy. |