Question: 454 Sequencing With Bwa Mapping
2
gravatar for Gabriel Wajnberg
9.1 years ago by
Gabriel Wajnberg70 wrote:

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

samtools visualization bwa igv • 2.7k views
ADD COMMENTlink modified 8.8 years ago by 2184687-1231-83-5.0k • written 9.1 years ago by Gabriel Wajnberg70
6
gravatar for Istvan Albert
9.1 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

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)

ADD COMMENTlink written 9.1 years ago by Istvan Albert ♦♦ 84k
3
gravatar for 2184687-1231-83-
9.1 years ago by
2184687-1231-83-5.0k wrote:

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?

ADD COMMENTlink written 9.1 years ago by 2184687-1231-83-5.0k
1

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

ADD REPLYlink written 9.1 years ago by Gabriel Wajnberg70
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