I have a number of gene sequences obtained using illumina sequencing and they are in fasta format, where nucleotides with a score of <20 have been replaced with X. I am going to filter my sequences by removing sequences that have 50% X's however would simply removing any X's in each read be a better method?
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By removing any X's in each read, do you mean for example ACGTXXACGT -> ACGTACGT? That would be a bad idea since you'd be deleting two (poor quality) bases. -
Hi Maubp,
Yes thats what I mean I wasnt too sure if it would be a bad idea or not but you have put my mind at ease. Thank you for the reply!Comment
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