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How to use bam file with a reference to visualize a gene and its location.

asked 2023-01-30 12:28:55 -0700

Vibha Tripathi gravatar image

Hi there, I am new user of genome browse. I want to see the alignment and location of some genes whose counts are differed during gene count from two different mapping methods. I want to visualize those genes and their proximities.

For that, I picked a ref. genome and a relevant .bam file (by File > plot > browse, the location and the bam file) on the genome browse page but it shows "Data for this zoom level is unavailable until background computation is complete. Try zomming in". What does it mean? I looked in the manual but could not infer the solution of my problem. Please suggest me how to properly visulaize a mapped (.bam) file with a reference geneome. Thank you.


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answered 2023-03-26 18:28:00 -0700

At wider zoom levels, GenomeBrowse needs an extra "precomputed" coverage file to be available for a BAM file to display coverage. A little "play" button should be in the top-left of a plot to start the computation to compute and write the .bam.covtsf file alongside the BAM file to display this coverage.

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Asked: 2023-01-30 12:28:55 -0700

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Last updated: Mar 26 '23