Extracting aligned consensus sequences for every transcript from sam file

Question

[EVR]

Hi,

I am new to RNA seq data anaylsis. I have a RNAseq data which I have aligned against transcriptome using bowtie2.

bowtie2 -x /bowtie2_index Sample.fastq -S Sample1.sam

Is it possible to get the consensus of all aligned sequences for every transcript like this

>transcript_1

actattactctatactcatcatctactactactactactactcaa..

>transcript2

atgctagctagctacgattggatgcagtctatagcgatgtaa....

Kindly help me. Thanks in advance

[GouthamAtla]

What would like to do at the end ? What exactly you want ? Do u just want all the aligned sequences in a fast format or consensus of all the aligned sequences or something else ?

[EVR]

Hi,

I dont want all the aligned seuquences but only the the consensus of all aligned sequence for every transcript.