Hi I recently got 3 sample WGS for snp analysis from same genome I seen my fastq file it has N . So how should i tackle this if i do not trim this and take it for mapping onto my reference genome will the aligner ignore this N while mapping??
Total number of bases 45191688940 Number of base N 884912
also the total number of bases in all 3 sample is different ? How is this possible when sequencing was done for same genome of different samples
s1_R1 s1_R2 s2_R1 s2_R2 s3_R1 s3_R2
45191688940 45191688940 43709052900 43709052900 53171402300 53171402300