I have performed mRNA seq for few samples and analysed them by using edgeR pipeline. Here I am looking for one particular trancript's expression profile. After analysis I find out that it is not expressing at all in any sample. This transcript does not have single read matching from the data set after featureCount analysis.
but when I did tblastx with the trinity denovo fasta file, this transcript is present there. which means there is a transcript present matching exactly with the query transcript that I am looking for. This means there are some reads present corresponds to my query transcript. but this is not being detected by the edgeR pipeline.
can somebody please tell me how can I retrive all the fastq reads corresponding to the perticular transcript from fastq file?
thank you in advance.