Question: converting local sra file to fastq
0
gravatar for ywwangkevin
2.0 years ago by
China
ywwangkevin0 wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.0 years ago by apelin20460 • written 2.0 years ago by ywwangkevin0
1
gravatar for Antonio R. Franco
2.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco3.4k wrote:

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 syncronized. Some aplications require so

ADD COMMENTlink written 2.0 years ago by Antonio R. Franco3.4k

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? 

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by ywwangkevin0
0
gravatar for apelin20
2.0 years ago by
apelin20460
Canada
apelin20460 wrote:

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

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by apelin20460
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 600 users visited in the last hour