Question: Browser to display sequence searches in BAM files
0
gravatar for hyanwong
5.8 years ago by
hyanwong70
United Kingdom
hyanwong70 wrote:

I have a large BAM file containing reads from a single human genome. I'd like a visual map of the locations of a specific 120bp nucleotide sequence. I've been using the IGV browser which allows you to find and display motifs in the hg18 reference sequence, but I can't find how to search for them in the sequence indicated by the BAM reads. 

I'd also like to do the same for the HuRef (Craig Venter) and Jim Watson sequences, to illustrate individual-level polymorphism for a lecture. Can anyone point me to suitable software?

ADD COMMENTlink written 5.8 years ago by hyanwong70

Are you looking for positions or motifs? You can just jump to a position in genome easily enough.

ADD REPLYlink written 5.8 years ago by Devon Ryan94k

Sorry - didn't make that clear. I'm looking for motifs (first 120 bp of the longwave and medium wave opsin genes. I only expect to find 3 or 4 hits (although some humans have up to 14 tandem repeats of this gene)

ADD REPLYlink written 5.8 years ago by hyanwong70

You can just blast the sequence and use the built-in map viewer. It's not as slick as IGV, but it gets the job done (btw, I can confirm that there are 4 hits in the current reference).

ADD REPLYlink written 5.8 years ago by Devon Ryan94k

Thanks. When you say "built-in map viewer" do you mean in UCSC Genome Browser? I'd prefer to search the BAM files using software on my own machine rather than have to upload them anywhere. Apologies for the basic questions: as I'm sure you can tell, I'm a complete neophyte here.

ADD REPLYlink written 5.8 years ago by hyanwong70

No, the online blast has a "map viewer" where you can see where the various hits align. Just blast the first 120bp and you'll find a link to the right of the hits. It's not the UCSC genome browser (it it were, I would have written that).

What I suspect you actually want to do with your BAM files is to create a reference sequence from them and then look for motifs of whatever for in that. In which case, just make the genome, search with blast or an aligner against it locally and then load the results (just make them a BED file or something, depending on your needs) and load that into IGV.
 

ADD REPLYlink written 5.8 years ago by Devon Ryan94k
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