Another great tool is RSeQC

I agree with Ashutosh Pandey

RSeQC works good for me

You need to download it run with

read-distribution-py -i your bam -r Refseq.bed

refseq.bed also you can download from their site according to the genome version you have

hth

I use RNA-SeQC from the Broad Institute.

As you pointed out, this being a Broad tool it is quite finicky with its requirements of what a Bam should look like. So this is what I do to prepare bams from Tophat for RNA-SeQC:

1. Index Fasta:

   ## I need to do this in the cluster I use to add the libraries to path
   export JAVA_HOME=/usr/lib/jvm/java-6-openjdk-amd64/jre
   export PATH=/usr/lib/jvm/java-6-openjdk-amd64/jre/bin:$PATH
   
   fasta="coolgenome.fa"
   
   java -jar ~/bin/picard-tools-1.119/CreateSequenceDictionary.jar R=$fasta O=${fasta/.fa/.dict}
   

2. Add read groups and index Bam

   aln="somemapping.bam"
   exp=$(basename ${aln%%.bam})
   
   java -Xmx6g -jar ~/bin/picard-tools-1.119/AddOrReplaceReadGroups.jar \
   I= $aln \
   O= ${aln%%.bam}.so.rg.bam \
   SO= coordinate \
   PL=illumina \
   PU= sample \
   LB= $exp \
   RGSM= $exp  2> $aln.sort.err
   
   # index bam
   samtools index ${aln%%.bam}.so.rg.bam
   

3. Pre-run Checklist

   #    Are the contig names consistent between your BAM, Reference, and the GTF file?
   #    Is your BAM indexed? (use samtools index)
   #    Is your reference Indexed? (use samtools faidx)
   #    Does your reference have a dict (dictionary) file? (use CreateSequenceDictionary.jar)</pre>
   

4. prepare sampleFile.txt

   printf "Sample ID \t  Bam File \t  Notes\n" > sampleFile.txt
   for b in */*.so.rg.bam; do
   sample=$(basename `echo $b | cut -f1 -d"."`)
   echo $samplef
   printf "$sample \t  $b \t \n"  >> sampleFile.txt
   done
   

5. Run the thing

   gtfFile="thegeneannotation.gtf"
   
   java -jar -Xmx5g ~/bin/RNA-SeQC_v1.1.8.jar -s sampleFile.txt -t $gtfFile -ttype 2 -r $fasta -o ./qcReport -gatkFlags "-S SILENT"
   

Some of these steps are needed only once the others I have included in my mapping scripts - I always output sorted and indexed bams for instance. I hope it works.