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.
I failed at the second step, the splice result is poor. The splicing software i used is NOVOPlasty.
Did someone have any suggestions？
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?
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.