I thank you for your help. I think I have understood why there is a mismatch. I run de novo assembly (on Vicia faba available SRA) using trinity on Indiana instance of galaxy and obtain results of transcriptome assembly as of set of 361,316 contig, they are all under an identifier beginning with TR1,TR2 etc.I then upload this file onto usegalaxy for SNP discovery. I have developed a workflow for SNP discovery. Following this workflow the first step is to align my dataset with this trinity assembled file (uploaded after de novo assembly) as a reference which I do by using BWA-MEM. I get output in BAM format and when I loading it to view in IGV I see it is a mismatch (as I have queried you earlier). However when I align them to my own reference (which is Medicago genome) I do get an output again in BAM format. When I visualize this under IGV I can see it clearly. I did FASTA manipulations to match the identifiers but this made no difference to visualization in IGV. Well this makes me think that when I align my dataset with reference I think IGV is not able to read as it takes those identifiers TR1 etc as unidentifiable. On the other hand when I align it with reference genome (Medicago) it gets identifiers like IMAG etc.. which is identified by IGV. So I think galaxy and IGV not recongnising the identifier is a problem.
I am not sure what I am thinking is perfectly fine. But I think to a great extent is a good explanation.
Could you please help me in this regard and suggest me other tools by which I can align my datasets with Trinity assembly as a reference?
Looking forward to reply from you.