Question: SRA to fastq
0
gravatar for lmobuchon
12 months ago by
lmobuchon10
lmobuchon10 wrote:

Hi everyone,

I tried to convert SRA to fastq using SRATOOLKIT 2.6.3, fastq-dump. The archive is from a ChIP-seq (single reads). This is my command line:

./fastq-dump --split-3 $DIR/SRR3722567.sra > $DIR/SRR3722567.fastq

It produces a fastq file which is empty (Written 34892751 spots for $DIR/SRR3722567.sra). I also tried the option --split-files but it produced error. How can I do ?

Thanks a lot for your help !

Lenha

sequencing • 525 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by lmobuchon10
1

Did you try without redirecting it into a new file?

ADD REPLYlink written 12 months ago by venu4.5k

Thanks you very much ! I used ./fastq-dump SRR3722567.sra and it works ! :)

ADD REPLYlink modified 12 months ago • written 12 months ago by lmobuchon10
1

Simply use the identifier SRR3722567. fastq-dump is quite lenient with cutting off parts of the identifier it doesn't need, though

ADD REPLYlink written 12 months ago by Michael Dondrup43k
0
gravatar for Michael Dondrup
12 months ago by
Bergen, Norway
Michael Dondrup43k wrote:

fastq-dump duesn't write the fastq files to standard out, instead it creates files in the working dir by default (and creates cache files in you home under ncbi and doesn't remove them either). Look for a file named SRR3722567.fastq in your working dir. See the help for more information.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Michael Dondrup43k
0
gravatar for Santosh Anand
12 months ago by
Santosh Anand3.0k
Santosh Anand3.0k wrote:

Why are you using "--split-3"? It's a single end sequencing https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3722567

Simply run

$ fastq-dump  SRR3722567

and it should create SRR3722567.fastq in the current dir.

ADD COMMENTlink written 12 months ago by Santosh Anand3.0k
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