Question: Where can I get fastq sequence files of length 150 and more.
0
gravatar for Agaz Hussain Wani
15 months ago by
India
Agaz Hussain Wani40 wrote:

I want to perform alignment of the human sequence reads with the reference genome. I need reads length 150 and more (500) to test some algorithm. Where can I find such type of reads, both single and paired-end. I got reads from 1000 genome project around 100 length, however I want reads of length more.

sequence alignment • 679 views
ADD COMMENTlink modified 15 months ago by bioExplorer3.7k • written 15 months ago by Agaz Hussain Wani40
3
gravatar for Gungor Budak
15 months ago by
Gungor Budak230
Ankara/Turkey
Gungor Budak230 wrote:

Use Sequence Read Archive advanced search and provide read length as 150 and species as Homo sapiens. You can add more filters if you want. The query should look something like this:

(150[ReadLength]) AND "Homo sapiens"[orgn:__txid9606] 

And here is a result for paired-end sequencing data with read length 150.

ADD COMMENTlink written 15 months ago by Gungor Budak230

Agaz,

If transcriptome reads generated from Pacbio interests you then you can access European Nucleotide Archive accession PRJEB3969 (https://www.ebi.ac.uk/ena/data/view/PRJEB3969)

ADD REPLYlink modified 15 months ago • written 15 months ago by toralmanvar750
1
gravatar for bioExplorer
15 months ago by
bioExplorer3.7k
bioExplorer3.7k wrote:

This is a very basic requirement and a lot of tools are available to simulate artificial reads from the genome under question. More interestingly, you can define the number, length and quality of reads also. One such well documented program ( ArtificialFastqGenerator )is here

Here is the publication link

Another very sophisticated tool is ART (courtesy: Biostars Handbook) which can mimic the sequencing platforms very well.

ADD COMMENTlink modified 15 months ago • written 15 months ago by bioExplorer3.7k
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