Question: IGV not reading BAM file
0
gravatar for novice
2.9 years ago by
novice830
United States
novice830 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 • 1.5k views
ADD COMMENTlink modified 2.9 years ago by ablanchetcohen1.2k • written 2.9 years ago by novice830
3
gravatar for ablanchetcohen
2.9 years ago by
ablanchetcohen1.2k
Canada
ablanchetcohen1.2k 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 COMMENTlink written 2.9 years ago by ablanchetcohen1.2k

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

ADD REPLYlink written 2.9 years ago by novice830

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 REPLYlink written 2.9 years ago by h.mon22k

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

ADD REPLYlink written 2.9 years ago by novice830
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1166 users visited in the last hour