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.
Question: IGV not reading BAM file
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novice • 890 wrote:
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modified 3.1 years ago
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ablanchetcohen • 1.2k
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3.1 years ago by
novice • 890
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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".
What's it with my name that's so upset you? Anyways, you solved my problem; thanks!
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.
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