fastq splitter is not working on paired end read for some of my file and produce output file with nothing in it but it is working properly on another file? i want to use the file in tophat. also when i tired to use tophat with option paired end as collect it do not take the file even after running fastq groomer on the file therefore ever time i have to split the file. now what to do in this regard?
If you are still having this problem with the splitter tool, the fastq FAQs here should help sort out the formatting problem: https://galaxyproject.org/support/#getting-inputs-right
Should the issue remain and you can reproduce it at Galaxy Main https://usegalaxy.org, a bug report from the error dataset can be sent in. Make sure the inputs and outputs are undeleted and include a link to this Biostars post in the comments.
All support FAQs: https://galaxyproject.org/support/
Thanks! Jen, Galaxy team