Fastq file and Fa file,How to create?

Question

[jafarzadeh91]

I need working with a program that get pair-end reads as a .fastq file and a reference sequence as .fa file.I want to test this program but I don't know how to create a simple .fastq paired end read file and also a .fa reference sequence file.I would be appreciate if provide me some materials about that or even provide me with 2 sample files(a .fastq paired end reads file an a .fa file containing a sequence as reference).

Thank you .

Answer 1

[Devon Ryan]

Just download some files from SRA or ENA and then get the associated genome from Ensembl or UCSC.

[jafarzadeh91]

Thank you.Is there any material on how to create them?the examples on that website are so complex to use as a sample for me.thanks

[Devon Ryan]

You could just download the genome for E coli or something else small and just generate fastq files from a simulator (just google "fastq simulator").

[Ashutosh Pandey]

I think it would be good to play with real fastq file generated from a sequencer rather than generating it form the reference sequence. Try ENA instead of SRA as ENA provides fastq.gz files instead of .sra files. This will save your time. As Devon said "you can then download the genome from UCSC". Google "ftp mm10 mouse ucsc" or any other organism depending on your fastq file. If you don't want to go this way then there is a tool that creates artificial fastq files from your reference of interest. See this: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049110