I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the samples. Can I spilt them from the one I have or I have to do tophat2 for all the samples separately? If yes, how to do it.
I need them for FRASER (splicing detction) I would also appreciate if anyone used FRASER before could help me a bit to get started. I am working with plant data for the first time.
The command I used
tophat2 -p 40 \ -o tophat_output_final bowtie_indexes/Medicago1/Medicago \ NRNSA_S103_R1_001.fastq.gz,NRNSB_S107_R1_001.fastq.gz,\ NRNSC_S111_R1_001.fastq.gz,NRSA_S104_R1_001.fastq.gz,\ NRSB_S108_R1_001.fastq.gz,NRSC_S112_R1_001.fastq.gz,\ RNSA_S105_R1_001.fastq.gz,RNSB_S109_R1_001.fastq.gz,\ RNSC_S113_R1_001.fastq.gz,SRAB_S106_R1_001.fastq.gz,\ SRB_S110_R1_001.fastq.gz,SRC_S114_R1_001.fastq.gz \ NRNSA_S103_R2_001.fastq.gz,NRNSB_S107_R2_001.fastq.gz,\ NRNSC_S111_R2_001.fastq.gz,NRSA_S104_R2_001.fastq.gz,\ NRSB_S108_R2_001.fastq.gz,NRSC_S112_R2_001.fastq.gz,\ RNSA_S105_R2_001.fastq.gz,RNSB_S109_R2_001.fastq.gz,\ RNSC_S113_R2_001.fastq.gz,SRAB_S106_R2_001.fastq.gz,\ SRB_S110_R2_001.fastq.gz,SRC_S114_R2_001.fastq.gz