how to know the isoform length and exon number of particular gene from rna sample

Question

[priyadhawan11234]

I have 4 sample of rna seq data(control and disease). i did alignment with STAR and RSEM to get the count matrix. now i want to know the size of isoforms in both cases of particular gene? how can i get this?

[priyadhawan11234]

thank you for the reply.

[ATpoint]

Please use ADD COMMENT and not the answer field to keep the thread logically organized.

Answer 1

[Kristoffer Vitting-Seerup]

You simply look it up in the the annoation you used tu build the index for RSEM. If you used a fasta file you can look up the isoform length (as it is the same length as the number of nucleotides for that entry). If you want the number of exons you will have to download the corresponding GTF file and extract the information from there.

[priyadhawan11234]

I used fasta file for RSEM. I got the transcript length from fasta (that is 6400 bp long). how can i get that sequence from bam file ?

[Kristoffer Vitting-Seerup]

Sorry but I do not understand what you want to do. Could you elaborate - and also please comment on why the nucleotide sequence in the fasta file is not good enougth?

[priyadhawan11234]

i just want to know which isoforms of particular gene are expressed in both sample and what is length of those isoforms. so how can i get that information from bam file generated by STAR?