I have RNA-seq data from different experiments. How can I analyze multiple samples together using tophat? I tried command as below
tophat -o output_dir --solexa1.3-quals --num-threads 12 hg19 rna_seq/raw_data/cancer_sequence.txt,rna_seq/raw_data/control_sequence.txt"
It seems the result only has one .accepted_hits.bam file and one junctions.bed file. I thought there should have different outputs for each sample. Should I run tophat for each sample separately??
Thanks!
tophat -o output_dir --solexa1.3-quals --num-threads 12 hg19 rna_seq/raw_data/cancer_sequence.txt,rna_seq/raw_data/control_sequence.txt"
It seems the result only has one .accepted_hits.bam file and one junctions.bed file. I thought there should have different outputs for each sample. Should I run tophat for each sample separately??
Thanks!
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