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GEO SRA files

Hey guys,

I am going to aligning reads from GSE35641 (http://www.ncbi.nlm.nih.gov/Traces/sra/?view=search_seq_name&exp=SRX119208&run=&m=search&s=seq), on ecoli reference genome (NC_000913). There are 6 sra files in GEO which the least size is more than 2G. Do you know any way to download the files faster? I need many hours to download a file of them in fasta format

Thank you biostars

sra rna-seq
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updated by Ram Ram • written by zizigolu zizigolu

2 answers

Look at using aspera from the command line or, if you are using R, as described in sections 3.5 and 3.6 of the SRAdb vignette.

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updated by Ram Ram • written by Sean Davis Sean Davis

Thank you

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updated by Ram Ram • written by zizigolu zizigolu

Yep, install Aspera and run it as follows:

ascp -i $KEY/asperaweb_id_dsa.openssh -k 1 -QT -l 200m \
  anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR390/SRR390728/SRR390728.sra \ # url for the file
  ./ # save location

$KEY should point to the directory containing asperaweb_id_dsa.openssh (it will be in the installation directory). See instructions here.

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updated by Ram Ram • written by arnstrm arnstrm

Sorry, is the command the same for Windows? I am not familiar with unix/linux.

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updated by Ram Ram • written by zizigolu zizigolu

Thank you,

I did all the steps but said that remote host not specified.

On the other hand if at last I could download, I need fastq or fasta, then can I download in these format or just sra?

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updated by Ram Ram • written by zizigolu zizigolu

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