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Question: IGV not reading BAM file
0
gravatar for novice
3.4 years ago by
novice • 920
United States
novice • 920 wrote:

I'm having a problem visualizing a BAM file with IGV. The file was generated with bowtie2 + samtools and can be viewed normally with BamView. IGV, however, doesn't read it; it just shows it as an empty track. Has anyone had this problem before?

I used the same reference with IGV as the one I used for alignment. I also do have the index file in the same directory as the BAM file.
igv bam alignment • 1.8k views
ADD COMMENT • link •
modified 3.4 years ago by ablanchetcohen • 1.2k • written 3.4 years ago by novice • 920
3
gravatar for ablanchetcohen
3.4 years ago by
ablanchetcohen • 1.2k
Canada
ablanchetcohen • 1.2k wrote:

The most frequent novice error is not to zoom in.

Just type in the name of a gene of interest and press "Enter".
Or select a chromosome, and a region of interest, then use the "+" sign to zoom in in the top right corner.

This answer is based on your handle, "novice".

 
ADD COMMENT • link written 3.4 years ago by ablanchetcohen • 1.2k

What's it with my name that's so upset you? Anyways, you solved my problem; thanks!

ADD REPLY • link written 3.4 years ago by novice • 920

Nothing in your name is upsetting. However, ablanchetcohen provided answers according with it (e.g. press "Enter"). Other novice mistake: not searching the forum before posting - if you did, you would find this and this posts.

ADD REPLY • link written 3.4 years ago by h.mon ♦ 26k

Good job explaining the explaining the situation in here, h.mon! Your comment was surely important and informative.

ADD REPLY • link written 3.4 years ago by novice • 920
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