Question: (Closed) SRR data assembly
0
gravatar for shamsurrahaman132
13 months 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 • 334 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 13 months 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 13 months ago by genomax92k

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

ADD REPLYlink written 13 months ago by shamsurrahaman1320

The link you posted above is downloading data, correct?

ADD REPLYlink written 13 months ago by genomax92k

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 13 months ago by shamsurrahaman1320

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

ADD REPLYlink written 13 months ago by genomax92k

Yes. Can you tell me how to download them?

ADD REPLYlink written 13 months 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 13 months ago • written 13 months ago by genomax92k

Hello shamsurrahaman132!

We believe that this post does not fit the main topic of this site.

Seems to be solved? Or at least not maing progress, therefore closed.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 11 months ago by ATpoint41k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1131 users visited in the last hour