Thanks for your reply.
I have one more question about the two-pass mapping.
I have 24 RNA-seq samples with 4 conditions from C.elegans, and 6 replicated for each condition. And I want to detect the alternative splicing events using these samples. I used the two-pass mapping in STAR.
For the first round, I used the default setting and got the SJ.out.tab from each sample.
For the second round, I built the genome index for each sample separately:
STAR --runMode genomeGenerate --genomeDir genome_index2
Then I did the second mapping using the sample-specific genome index2.
However, in the manual it's recommended to concatenate the SJ.out.tab files from all samples together and build the same genome index for all the samples.
I am wondering if this difference will influence a lot? Do you recommend me to redo the second mapping as suggested in the manual?