454 Sequencing With Bwa Mapping

Question

[Gabriel Wajnberg]

Well, I indexed my ref.fasta of hg19 (using bwa index -a bwtsw database.fasta) , and mapped my fastq file using bwa, using ( bwa bwasw database.fasta long_read.fastq > aln.sam )... converted my sam to bam.... using samtools and then I tried to visualize in UCSC custom track and IGV...and appeared nothing like this screenshot : http://www.4freeimagehost.com/show.php?i=776af632ebca.png

so why is it happening ??? thanks

Answer 1

[Istvan Albert]

This is actually very counterintuitive (and burned me as well the first time I used IGV) - if you are zoomed out too far then IGV displays nothing ... there should be a more prominent indicator that the content is not shown (you have that small text there that asks you to zoom in)

Answer 2

[2184687-1231-83-]

Just to confirm, if you do a "samtools view mybam.bam | head" and look at the coordinates for the first 10 lines (third and fourth column), then zoom in to those coordinates in IGV? Is it still blank?

[Gabriel Wajnberg]

thank u both.... helped me a lot :))