Entering edit mode
6.9 years ago
novicebioinforesearcher
▴
70
I am trying to plot logos using consensus matrix and pwm from biostrings and seqlogo package in R. First based on certain co ordinates I obtain fasta sequence using bedtools getfasta option
sequence1 TTGAATAATGTCTTCATGTTTAGAATCAT
sequence2 tgaaatgcaCCTGTCTTTTCTAGAAGAGA
sequence3 GAGTAATGTGGATTTCATTTTAGAAGCAA
sequence4 TAAAAAAAACTTTTTACTTGTAGATGAAG
sequence5 CCCTTTTTCACTTTTTTCCCTAGCAACTT
sequence6 ATCATGGGAATTCTTTCTTCTAGCGCTGA
sequence7 TCTAGCCCCTCCCTCCACCGTAGGTTTGA
sequence8 TATTTCTGTTCTCTATGTCAATAGGAAGA
sequence9 TTCTAACTTCTCTGTTTTCTGTAGGAAGT
sequence10 TATGTTGTTTGATTGCGTTGTAGGAAGAT
sequence11 ATCTCCCTGTTTTTTTTTCCTAGATGACA
sequence12 GATAGTCCGTCTCATGTCCCTAGGTCAGA
sequence13 ATATACTACCAGTTTCAGGATAGTCCGTC
sequence14 AGTTTGTTATTTTTCAACCATAGAAGCCA
sequence15 GACAGCTAATGTTTTGTCTGATAGGTATT
sequence16 GGGATTTTTATTTTTACAATTAGGAAAAG
sequence17 TTAAGAACTTCTTTAAATTTTAGGTCAAG
sequence18 TCACAAGCATTTTTAAAATTTAGGAGCTC
sequence19 GAAGGTATTTTATGTTTTTAATAGTGAAA
sequence20 TTCTTTCCTCAATTCATTTTCTAGCATTG
sequence21 AACTTCCTACGTGCCCCTCCTAGCTCTCC
sequence22 GTCTTTCCTAAATTCTCTGCCAGTTTGGG
sequence23 tttttaattttGATCAATTTTAGATTTCC
My question is do i need to change letter that are lowercase? will it affect my logos plot or the pwm calculations?
Thanks
just ..... try ?