Use distinct fastq datasets for pair-end use of Tophat. Meaning, do not use a joined file that contains both ends of the reads.
Be sure to double check the quality score scaling, if you have not already, before assigning the "fastqsanger" datatype to the inputs. Here is how:
Best, Jen, Galaxy team
I am not able to understand:
i have 2 samples ( eg A with R1 and R2 and B with R1 and R2)with forward and reverse reads respectively since they are of the same length so i joined the reads from sample A by using FastQ joiner
Now i have one single file( Fast Q joiner A)
my question is: Now i want to run tophat on these samples:
a) can i use this joiner file as an input and advise what should be my customised parameter like i will select paired end read then tophat asks for forward and reverse files but now i have one single file (obtained from Fastq joiner)
b) if i cant use this file then whats the advantage of using this feature kindly advise am very confused.
c) i tried running tophat by changing the parameter as paired end read and by selecting paired end collection but for this do i need to change the file format again or should i use paired end individual dataset then i don't see the utility of fast q joiner output