I have some non-coding region sequence around 5000 and some tissue specific reads data. I want to do differential gene expression analysis. So I want to check which tissue specific reads having these non coding sequences for that I aligned them (where I created database for those non coding sequences) by tophat2. Then I need to have count file from these bam file, used featureCount but it gave zero only.I also used bedtool also it also not worked. I suspect because of those non-coding seq it can't generate count file...may be I don't know. I convert bam to sam file then it looks like this:
> @HD VN:1.0 SO:coordinate @SQ SN:0 LN:309 @SQ SN:0 LN:381 @SQ SN:1 LN:1085 @SQ SN:1 LN:353 @SQ SN:10 LN:239 @SQ SN:10 LN:205 @SQ SN:10008 LN:659 @SQ SN:1001 LN:291
Can you people tell me what should I do?