Is there any tool which can recognize and replace dye blobs with N in Sanger ABI files?
I haven't worked with Sanger reads yet, maybe it is not such a problem not to do anything with them, will it make problems while mapping?
Just in case anyone reads this question years later, the way to solve this problem is to rebasecall the .ab1 file (you just need to load it back into Sequence Analysis or ask your sequencing facility to do it for you) and up the N base threshold value. Regions of dyeblobs have low quality scores and by increasing the N base threshold you will turn the low quality bases into N.
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