visualizing alignment using IGV and WIG file

[Ashley]

Hi,

  I would like to visualize the alignments from my rsem-calculate-expression run.  I ran rsem-bam2wig using the following command:

rsem-1.2.3/rsem-bam2wig /data/scratch/aeb5/s_1_nopolyA_single/s_1_nopolyA_single.transcript.sorted.bam s_1_nopolyA_single.wig s_1_nopolyA_single_wiggle_plot

This seemed to run fine, and it generated a file called:  s_1_nopolyA_single.wig (as expected)

However, when I load this onto IGV, only some of the contigs align.  Why is this the case?

Did I run rsem-bam2wig wrong?

Should I convert the WIG file to a tdf file?

Is the problem due to the fact that I couldn't provide a GTF-formatted annotation file since I am using a de novo transcriptome?

Any input is more than welcome!  

Thanks,

Ashley 

                                    

[Brian Haas]

Hi Ashley,

Just out of curiosity, are you able to load the bam file into IGV and do you see reads aligned for those contigs?

                                    

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Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas

 

[b...@cs.wisc.edu]

Hi Ashley,

If your wig file is not large enough, it is fine to use wig format.
otherwise, I suggest you convert it to tdf format.

Please see

c) Loading a BAM and/or Wiggle file into the UCSC Genome Browser or
Integrative Genomics Viewer(IGV)

from
http://deweylab.biostat.wisc.edu/rsem/README.html

for more details.

Best,
Bo