cleaning up illumina data

[Javid]

Hi there,

I have recently received my illumina sequence data (Paired-ends module) which are transcriptome. I have done the fastqc analyses for a quality control assessment of the data which was good. As I am using the windows platform, I would like to know which softwares can be used for cleaning up the paired ends sequences? some people are using Tagcleaner (Standalone version) which is designed for linux platform users not for windows. The Trimmomatric is the pipeline software which can be used along with the Tagcleaner. Could you please introduce me some other clean up softwares for windows users?

Thanks
Javid

[pbluescript]

If you don't have access to a Linux machine, you can use the fastq manipulation tools under Galaxy.

[JackieBadger]

Just download VMplayer and run ubuntu through it.... hey-presto you have a linux virtual machine on your windows machine

[Javid]

Thanks colleagues,
I need to check the programs you introduced to see if they work for my data.

cheers
Javid