我正在尝试使用 fread 将基因组比对读入data.table
R 中。这是比对文件的快照:
USI-EAS28:1:100:1786:674#0/1 + 1_maternal 68326824 CTCAATTATACTGAAAGAAACACAATATATCATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1786:940#0/1 + 16_maternal 11407541 CTATTAGTGACCTGCTGTGGGACCTTGGGATGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1786:705#0/1 + 1_maternal 63849584 CTGAGGGTTTGTGTCAGGAAGGGGTGTGGAATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0:T>C
USI-EAS28:1:100:1786:1168#0/1 - 5_maternal 31381649 GCATCATTCATGAAACAATTTTCAAGAGAGGAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1787:582#0/1 + 10_maternal 54587781 CTACAATAATAATAGGGGACTAAAACACCCCACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1787:62#0/1 + 10_maternal 70390747 CTATTTGCTACTGAATTGTTAATTTTAAAACAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1788:573#0/1 - 7_maternal 92583837 CACTGTCAACATTAGACAGACCAATGAGACAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1788:854#0/1 + 7_maternal 129611206 GTTTGTTTTTTTTTTTGAGATGGAGTCTCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 32:C>T
USI-EAS28:1:100:1788:185#0/1 - 13_maternal 23694307 CAAACAAACTCAAAATGGACTATCGACTGAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
USI-EAS28:1:100:1788:1339#0/1 - 13_maternal 33699510 TTAACTCTAGTTTTTAGGGATTGCAAATTAGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 0:A>G
第二列报告读取对齐的链(+
正向,-
反向)。不幸的是,fread 试图将这一列读入一个整数,并将该值始终赋值为 0。就此而言,这一列应该被读取为一个字符,甚至是一个布尔值。试图玩弄争论sep
并sep2
没有帮助。