How to read FASTQ files?

[Mr.Zurich1992]

Hi


I have sequenced my exomes by Genebygene in Houston, TX. I got now the exome data. But the exome data has FASTQ files. I can't use them. What I have to do?

[mastal]

How to read FASTQ files?

fastq is a common format for sequencing data, and most alignment programs (like BWA and Bowtie) use fastq files as input.

[Mr.Zurich1992]

I have to download BWA?

[Mr.Zurich1992]

It doesn't run.

[Bukowski]

http://seqanswers.com/wiki/How-to/exome_analysis

What on earth possessed you to do an exome experiment with no idea how to analyse the data? You do realise there are other sequencing providers that would do the alignment, variant calling, annotation and everything else for a modest extra cost on the capture and sequencing.

[Mr.Zurich1992]

I am not even able TO OPEN the exome data!

[Bukowski]

You don't 'open' exome data. It's probably compressed fastq files, they end in a .gz extension. These files are binary files and you are meant to align them to a reference genome as your next step. And yes, that means using BWA. Which works on Linux machines.. just in case you were entertaning the idea of trying to do it in Windows.

[mastal]

How to read FASTQ files?

What kind of computer/operating system are you using?

If you need a crash course in basic linux, see this tutorial:

http://www.ee.surrey.ac.uk/Teaching/Unix/

Your fastq files are probably compressed.
If they are of the format reads.fastq.gz, you need to do,
at the terminal prompt,

$gunzip reads.fastq.gz

if they are in fastq.tgz format,

$tar xvzf reads.fastq.tgz

[Mr.Zurich1992]

I'm using Winsows vista 32-bit and winrar

It doesn't run on Windows?


Anyway I'm looking forward to get the exome result variant, too.

[Bukowski]

A 32 bit machine wont even let you build the bwa index required to to do the alignment, so no you're not going to be able to analyse the data on a 32bit Windows machine.

Please go and seek out a local bioinformatician who can help you. I've analysed 1000's of exomes, and if you are doing it for the first time, you won't even get started without a 64bit Linux machines with a few GB of RAM and a full week to dedicate to understanding how it all works.

[JackieBadger]

Google is a wonderful invention, you know?

[Mr.Zurich1992]

Isn't possible I could convert the FASTQ files to bam files?


Cause there is a good program called Bamseek. Bamseek is able to read the FASTQ files, but the result is a big mess.

[JackieBadger]

BAM is an alignment file...FASTQ is not

[mastal]

fastq files are human-readable text files if you unzip/untar them.

aligners like bwa will output the alignments in bam (binary) or sam (the human-readable text equivalent of bam) formats, and you can use samtools to convert between bam and sam.

[Simon Anders]

Look, you already paid a company to do the sequencing for you. They gave you back the raw data, right as it comes out of the machine, instead of running it through the usual analysis pipeline. You can do this yourself, but it will take you at least several weeks to learn how to do that. Why don't you simply pay the company to do the analysis for you, too, and to provide you with a list differences between your sample and the mouse reference, if this is what you need.