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Old 05-12-2015, 02:02 PM   #9
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,048
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Quote:
Originally Posted by super0925 View Post
I downloaded from iGenome...
Do you mean my files is abnormal?
No. One of the reasons to get this data from iGenomes is it has (supposedly) been checked for consistency so the kind of thing you have run into does not happen. It is possible that you may have downloaded a flawed version that has since been fixed (you could download a new copy and compare).

I hesitate to recommend that you get sequences of missing fasta from NCBI and append them to your genome.fa file (you will likely need to re-index it again). But this may get you past one of the errors.

I am not sure how much work you have put into this already but if the new download from iGenomes does have these sequences then you could use that genome.fa file.

As for your second error this thread seems to have some options: https://www.biostars.org/p/57249/
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