converting scaffold to bam file

[khush]

hi

I have denovo assembled scaffold of a crop plant (genome seq not avaliable, only scaffold are avaliable online).
Is there any way i can convert this fasta format of the scaffold to bam file.

All I need is a pictorial view of these scaffold and check if these scaffolds overlap or not.

Thanks in advance.

[Brian Bushnell]

Converting to a bam file will not tell you whether there are overlaps. Actually, I'm not really sure what you are trying to do. Could you try to clarify?

You can find repetitive content, and get a visual representation of it, with a tool like MUMmer (align the assembly to itself). Also, I have a tool called Dedupe that can find overlaps between scaffolds, and display them as a graph.

[khush]

actually i was thinking to convert the fasta file into bam format so that i can view the scaffolds under IGV and check for overlapping scaffolds.

as far as my knowledge i think that assembled scaffold do not overlap. but i dont know if i am correct.. so to verify that i need to check that.

so if you could help me in converting my fasta format to bam format would be a great help.

thanks in advance.

[syfo]

The bam format is designed to represent genomic alignments of sequencing reads. Such alignments are typically generated by mapping reads on the genome with tools like star, bwa, etc. Since you have no reference genome a bam format is irrelevant here.
What you want to do is what Brian suggested above: align the scaffolds with each other. This does not require the same tools than for mapping reads and does not generate bam format.

[khush]

thanks syfo..