SRA to fastq

Question

[lmobuchon]

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

[venu]

Did you try without redirecting it into a new file?

[lmobuchon]

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

[Michael]

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

Answer 1

[Michael]

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.

Answer 2

[Santosh Anand]

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.