I am using Tophat for my analysis on RNA seq data After I ran Tophat on my reference geneome(which is basically for 80 ribosomal protein genes only) ,I got accepted_hits.bam and junctions.bed files as output in which i am interested.
I ran my tophat command on single end data Below is the code i used for it. First of all I align it and build index with bowtie using bowtie-build command
bowtie-build genomic_seq.fa GenomicRPGenome
(genomic_seq.fa is my fasta files for 80 ribosomal protein genes) Then i ran tophat command
tophat /Genomic_bowtie_index_files/GenomicRPGenome read1.fastq
In accepted_hits.bam , the value of mapping quality(column 5) is 255 which means that mapping quality score is not available. So does this mean that i did something wrong??
A junction file is also produced. The result for the junction file is not in accordance with the known splice sites. I don't know why this weird result came into the junctions.bed file. It would be very nice if someone could help me out in this. Am i missing something or doing something wrong. For the time being i am only dealing with single end rnaseq data
Thanks in advance