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Why is the coverage track not grey anymore?

asked 2020-09-08 06:58:02 -0600

Signe Neldeborg gravatar image

When opening BAM files in Golden helix genome browse 3.0.0 my coverage track is no longer grey (only colored if there is a variant present). Now, the bases are colored like in the reference sequence track (green, yellow, red and blue) and my variants are shown in the coverage track and no longer the pile-up track as it used to. Is this a new setting, and can I set it back?! The software is useless to me now, with these new settings.

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answered 2020-09-08 10:30:25 -0600

Hi Signe,

The coverage track is gray when the correct reference sequence has been detected and so we can evaluate the match of the BAM letters to the reference (gray meaning matching bases, colored when mismatching).

First thing to check is that you have the appropriate reference sequences downloaded. You may have deleted the local reference sequence or you may be looking at BAMs with new assembly builds.

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Asked: 2020-09-08 06:58:02 -0600

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Last updated: Sep 08 '20