Extracting Novel transcript sequence from RNA-seq alignment

[sahilsukla]

Hi everyone,

I have performed RNA-Sequencing Analysis for 4 samples with Illumina PE 100bp reads against Human (Hg19) genome using Avadis-NGS. We have detected few novel genes and most of them are differentially regulated across the samples. Now I want to extract the Novel gene sequences for further downstream annotation. What I have got from Avadis is just the genomic start & end coordinates without even strand information. I am wondering that extraction of sequence from genome using these coordinates will not make sense as it will be genomic sequence and not novel EST sequence.

I can export the alignment sam/bam file from Avadis. Is there some way to get the est sequences from sam/bam files?????

Can anyone please help me in this scenario

Thanks in anticipation.....