I have assembled de novo reference gene and mapped it to tophat now i want to calculate the read count for mapped reads.
For this, i sorted my bam files and used htseq count for counting the reads . I used the gtf file for this.
Ques 1. Htseq is giving 0 for every read count? Why ? But i can see a lot of reads in IGB. Please suggest a way to count the number of mapped reads
Ques 2. When i performed cufflinks with the same gtf file it gave a lot ensemble ids and FPKM but why is HTSeq not working in this case, it is identifying the ensemble ids but giving 0 for every ensemble ids.
What kind of programs can be used for this?