information regarding sequence characterisation

[mamtama...@gmail.com]

Hello everyone,

I figured out the deferentially expressed mode of a target gene in two different tissue. I wish to assemble tissue specific RNA-Seq corresponding to my target gene and want assemble them independently. I am trying to generate tissue specific contig for my target gene and then align all three contigs (Conbined contig+Tissue A specific contig+Tissue B specific contig) togather to see any changes. I tried CLC genomics work bench to assemble the reads but it could not be done as CLC need a threshold number of reads to assemble. I struggled to find a relevant approach to do so in available literature.

I have some concern regarding this

1- Is this an appropriate approach

2- Is there any assembler tool available that has no limitation of minimum read numbers.

Looking for appropriate advice.

Thank you in advance

Regards
Mamta