The cost of sequencing cost of library preparation & the cost of running the sequencer

I’m quite interested in the cost of sequencing for a genome. I read the
paper "The real cost of sequencing: higher than you think! " which published
on <Genome Biology>. It’s a good paper but the author didn’t separate the
cost of library preparation from the cost of running the sequencer. So my
question is from your experience, could you tell me the ration of the cost
of library preparation to the cost of running the sequencer. It’s quite
important for me to design a experiment.

as indicated in the paper, the two numbers you mentioned regard the cost of library prepration ($500) and the cost running the sequencer ($6000), respectively. Note that current figures may be different.

read cleaning for FusionSeq

The read cleaning (such as adapter remove, low quality base cut and polyA/T trimming) is required for FusionSeq? When we cleaned FASTQ file "SRR018259" which is publicly available, the FusionSeq cannot find correct fusions. On the other hand, when we run the FusionSeq without cleaning, it can find same fusions report in the paper. I would like to know which FASTQ (raw or cleaned) is recommended to load the FusionSeq.

And if cleaning is recommended, which is better to remove adapters.
(1) trimming adapters from reads (Read length is differ)
(2) removing the read itself (Read length is same)

thank you for interest in FusionSeq and for your note. We typically run
the programs on clean reads (i.e. without adapters), but we keep all
reads, regardless of the score. The filtering of potential artifactual
fusion transcripts is performed in subsequent steps within FusionSeq.
Please also note that the filtering step may require some tuning
depending on the specific library preparation protocol. Hence, I would
recommend to remove the reads that have adapters (no trimming).