inserting bases into the consensus?

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cjones
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Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
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inserting bases into the consensus?

Post by cjones » Thu Feb 19, 2015 1:13 am

One of my students has run into a problem in which the consensus shows 10 T's and a pad between two A's, but there are actually 12 T's there and Consed has simply misaligned things terribly. She can convert the consensus pad to a T (well, okay, a "t") but for the life of me I can't figure out how to insert the 12th one into the consensus. Any ideas?

Chris

wleung
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Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: inserting bases into the consensus?

Post by wleung » Thu Feb 19, 2015 7:15 am

One way you can insert a new base into the consensus is by inserting the base into one of the reads aligned to the position of interests and then change the consensus. Basically, you can open one of the traces and then select the base just after where you want to add a base in the "edt" line. Press the space bar to insert a pad and then edit the pad to change it into the new base (e.g. press "t" to change the pad to a low quality t). Then you can middle click on the new base and select the "Change Consensus" option to update the consensus sequence.

Alternatively, for regions with multiple sets of misaligned reads, you can pull out each set of discrepant reads and then use miniassembly to update the consensus sequence.

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