I am presently working on RNA seq paired end data from few Drosophila tissues. As I dont have an established genome reference I need to rely on reference free variant calling tools and I find KISSPLICE suitable. I have outputs generated for my datasets. I have few questions related to the outputs generated.
The paired end inputs as indicated in manual needs to be loaded separately as -r read.1 and -r read.2. A single output that is generated contains coverage as C1 and C2 for lower and upper path, do I have to sort the outputs to get information for my sample or the output that is generated is final output that I can rely on for that sample? Find the log file I have attached with this mail for one sample. I carried the same analysis by merging 2 fastq files into one file. I got slightly different outputs.
Are there any graphical representations options that I can apply to the outputs? I have a total of 6 paired end samples . What is the best possible method to quantify and compare these samples? source of samples are testis tissue from different species.