Question: small dataset for NGS pipeline
0
gravatar for joe
18 months ago by
joe0
joe0 wrote:

Dear bioinformaticians,

I would like to know if there is a small NGS raw data that can be used for analysis on a private PC.

The aim is to evaluate my pipeline (alignment, variant calling, annotation) and see if all commands are working before moving to the HPC.

Appreciated, Yousef

ADD COMMENTlink modified 18 months ago • written 18 months ago by joe0
1

Hello,

have a look at the European Nucleotide Archive for finding data that fits your needs. Maybe a sample of this study?

fin swimmer

ADD REPLYlink written 18 months ago by finswimmer13k
1

Along to @finswimmer's comment, to download from ENA Fast download of FASTQ files and metadata from the European Nucleotide Archive (ENA)

ADD REPLYlink written 18 months ago by Bastien Hervé4.7k

Hello,

Thank you for your reply.

This is a good start. I will try it.

ADD REPLYlink written 18 months ago by joe0
1

a small NGS raw data

You may want to elaborate on:

  • organism of interest (human?)
  • sequencing technology (illumina?)
  • size of dataset
ADD REPLYlink written 18 months ago by WouterDeCoster44k

I actually would like to know if there is clinical exome data available!

do you think clinical exome data will be exhaustive for the private PC?

thanks

ADD REPLYlink written 18 months ago by joe0

Why not take data attached to the publication of your interest ?

ADD REPLYlink written 18 months ago by Bastien Hervé4.7k
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