Min/Max allowable Ns in reads

[jfo]

Dear all,


How much Ns in a read should be allowed before discarding it? I have read a few studies removing reads with >1 N; but most studies on RNA-seq do not mention about this parameter. Is this too stringent for de novo assembly and differential expression studies using Illumina Hiseq 100 PE? All suggestions will be very much appreciated. Thank you!

[GenoMax]

N's appears in reads due to the inability of the basecaller to assign a specific base. In generally they should be rare/absent. You may see them in libraries with low nucleotide diversity. You obviously don't want them in data that would be de novo assembled. If they are present at the beginning/end of the reads and can be easily trimmed then you should remove them.