how to splice a gene sequence

Question

[linqide0418]

My Purpose

There are some sample Individuals with two phenotypes, dwarf and non-dwarf which all are sequenced. I need to splice the SMAD7 gene domain to distinguish whether different phenotypes samples gene have Insertions and deletions.

What I have

Only the sequence alignment bam file.

What I do

First, I extract fastq file from the bam file and align these with SMAD7 gene to ensure the position of the similar regions. Second, I extract fastq sequence from the similar regions and assembly it to get SMAD7 gene, then to distinguish whether different phenotypes samples gene have Insertions and deletions.

My problem

I failed at the second step, the splice result is poor. The splicing software i used is NOVOPlasty.

Did someone have any suggestions？

[liorglic]

I don't understand what you mean by "splice the SMAD7 gene domain" - can you clarify? what exactly are the inputs and outputs you expect?

[linqide0418]

the input is reads1.fq and reads2.fq，the expected output are assembled files. "splice the SMAD7 gene domain" is not right, I mean is assembly SMAD7 gene.