This is a test version of Biostars. For the public version, visit https://www.biostars.org.
converting local sra file to fastq

I am trying to convert .sra files to fastq using fastq-dump in Ubuntu. I have already downloaded the sra files. I used the command:

fastq-dump --split-files /home/ywwang/ncbi/public/sra/GSE52643/SRR1035695.sra

and I got the information below:

Read 33108579 spots for /home/ywwang/ncbi/public/sra/GSE52643/SRR1035695.sra
Written 33108579 spots for /home/ywwang/ncbi/public/sra/GSE52643/SRR1035695.sra

Does it mean the program have converted the sra file successfully? But I couldn't find the output file

fastq sra
• 5,654 views • link
updated by Ram Ram • written by ywwangkevin • ywwangkevin

2 answers

  1. Yes. It has to have created the corresponding files
  2. If you don't see the files, this is weird. I understand you have permission to write in that directory and/or you have free quota to use
  3. I recommend to use the --split-3 files instead, because it will ensure that your files are synchronized. Some applications require so
• 0 views • link
updated by Ram Ram • written by Antonio R. Franco Antonio R. Franco

Thanks, Antonio. I just couldn't find the output file if I used the command above.But I tried add output path to command and it worked. Does the program output file to the path where input file located if I use the command with no output path like above?

• 0 views • link
updated by Ram Ram • written by ywwangkevin • ywwangkevin

Hi, I am new to NGS and I am trying to convert .sra files into .fastq by the following command 

fastq-dump --outdir /opt/fastq/ --split-files /state/partition1/home4/rcms/abeera.fatima /ncbi/public/sra/ SRR3724452.sra

but it is not working and giving an error by generating an error file... what should I do now

• 0 views • link
updated by Ram Ram • written by abeerafatima121 • abeerafatima121

As a diagnostic, I would recommend:

fastq-dump SRA000000.sra --stdout > ~/SRA000000.fastq

This should work and should create the file in your home directory

• 0 views • link
updated by Ram Ram • written by apelin20 apelin20

Log in to answer this question.

More posts like this