Question: ATAC-seq many reads first base is "N"
26 days ago by
MatthewP • 780
MatthewP • 780 wrote:
I have fastq file of ATAC-seq but many reads start with one "N" base, I wonder what could be the reason.
@A00838:273:HCV7KDSXY:4:1101:1506:1000 1:N:0:AGGCAGAA+TATCCTCT NATCCAGAAAAAAAAAAAATCATGACCAAGCTTACCGTCCCCACTTAAAT + #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF @A00838:273:HCV7KDSXY:4:1101:1687:1000 1:N:0:AGGCAGAA+TATCCTCT NCATAGATCACATTAAGTACAAATATAAACAGTATTATTTCTTTACAATTGGATGTGTTGGAGACTTACTGATGT + #FFFFFF,FFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFF:FFF:FFFFF:FFFF,F,FFFFFFFFFFFFF:
Stats of such kind of reads:
$ zcat ATAC_R1.fq.gz | grep -e "^N" | wc -l 15150 $ zcat ATAC_R2.fq.gz | grep -e "^N" | wc -l 28
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