Question: SRR data assembly
0
gravatar for shamsurrahaman132
6 weeks ago by
shamsurrahaman1320 wrote:

Hello, I'm new in bioinformatics. I'm trying to assembly NCBI data. So, I have downloaded Staphylococcus aureus fastq file from NCBI. The downloaded file name was sra_data.fastq. The code I've used to download the data is : http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRR10231237&format=fastq
I'm using ABySS to assembly sra_data.fastq. I had studied ABySS documentation but unable to find solution. Please I need guidance

assembly • 139 views
ADD COMMENTlink written 6 weeks ago by shamsurrahaman1320

This appears to be RNAtag-seq data. Are you sure you need to assemble this rather than align to a reference?

ADD REPLYlink written 6 weeks ago by genomax74k

Thank you for the information. Can you guide me how can I download NCBI data?

ADD REPLYlink written 6 weeks ago by shamsurrahaman1320

The link you posted above is downloading data, correct?

ADD REPLYlink written 6 weeks ago by genomax74k

Yes it is but as you said earlier this is downloading RNA-seq data. I's looking for raw reads more like fastq files so that I can assembly them myself to learn

ADD REPLYlink written 6 weeks ago by shamsurrahaman1320

Those should be raw data i.e. fastq reads.

ADD REPLYlink written 6 weeks ago by genomax74k

Yes. Can you tell me how to download them?

ADD REPLYlink written 6 weeks ago by shamsurrahaman1320

Click on the link you included in your original post. Save the file that is downloaded. It will be gzip compressed and contain the fastq reads.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax74k
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