I have used FLASH to assemble some reads. They are still in FASTq format. However I can't get other tools to recognize that they exist.
So for example, if I try to use the FASTq to FASTa covert they are not in the list of files I can convert. Same with clip or cutadapt if I want to remove adaptors... they are not an option. These tools only recognize the original R1 and R2 files as being available in the history.
Has anyone got a solution or an explanation for this? I am sure I did this a few months ago and it did work.