extract transcript sequence from bam file to know transcript length in control and disease RNA samples

Question

[priyadhawan11234]

Hi

I am interested in extracting sequence of a transcript from a control and diseased sample. I have RNAseq data available and i am wondering how do people normally go about doing this with RNAseq data ? i want to know the the transcript length in both samples. Is there a way where you can extract the sequence from say BAM/SAM files?

[GouthamAtla]

transcript length in both samples: First why do you expect a different transcript length ? Because splicing and some exons skipped ? In that case, look for alternative splicing analysis like leafcutter, MAJIQ, rMATS etc

Another option is to assemble the rna-seq reads and look for differential transcripts in assembled transcripts.

If its not due to alternative splicing and for some other reason, align your reads to reference genome in both the samples and plot coverage across that specific transcript.

Otherwise please state what are you expecting from your data.

[priyadhawan11234]

Thank you for the answer. yes , i am expecting different transcript length because of splicing. my interest gene have 8 transcripts because of alternate splicing. so i want to know in both control and disease samples which transcripts are expressed and also if same transcripts, then size of the isoforms in both cases.

Answer 1

[GouthamAtla]

If its about splicing, try leafcutter , MAJIQ or rMATs etc depending on your convenience to identify differentially spliced transcripts