Hello,
I have recently been trying to align both RNA and DNA reads to a reference sequence using BWA and bowtie. While they have been working wonderfully for the DNA, the RNA is being handled with hostility.
The reference and the reads both contain Uracil but it seems that both BWA and bowtie think that Uracil is lame and subsequently convert it into Thymine or 'N'. I was looking at tophat as a way to solve my problems but before I spend time configuring it I wanted to get some input from people on this forum.
Example:
I want to align this:
agcgaguaaaagacu
against this:
ccucuuuccaucuacagcccacuggcacuccaggcaccuaccuacuucaaacaagcucaa
gccaaggccuuccccuaacucugacugcuagucccacaguaacccugacagcugcugcuc
cugcuucuccugaacagauuauuguucaugcuuuauccccagaacauuuguugaacacaa
gugauaauguuacagugcagugucacacaccaagagucaucauucagacuguugccacag
aggacaucacuucuuccauaucccaagcagaacugaccgucgauagugauauucagucau
cugauuuuccugagccuccagacgcccuagaagcagacacuuucccagaugaaauucauc
acccuaagaugacuguggagccaucauuuaaugaugcucauguauccaaauucagugaccaaaauagcacagaacugaugaauaguguuauggucagaacagaagaagaaaucucugaca
ccgaccuuaaacaagaggaaucacccucugauuuagccagugcuuauguuacugaggguu
uagagucucccacuauagaagaacaaguugaucaaacaauugaugaugaaacaauacuua
ucguuccuucaccacauggcuuuauccaggcaucugauguuauagauacugaaucugucu
ugccuuugacaacacuaacagaucccauacuccaacaucaucaggaagaaucaaauauca
uuggaucauccuugggcaguccuguuucagaagauucaaaggaugucgaagauuugguaa
acugucauuagaauaauucu
What is the best tool to do this. Please keep in mind that I have a very large reference sequence so speed is critical - One of the main reasons I went with a BWT based tool to begin with.
Thank you!
I have recently been trying to align both RNA and DNA reads to a reference sequence using BWA and bowtie. While they have been working wonderfully for the DNA, the RNA is being handled with hostility.
The reference and the reads both contain Uracil but it seems that both BWA and bowtie think that Uracil is lame and subsequently convert it into Thymine or 'N'. I was looking at tophat as a way to solve my problems but before I spend time configuring it I wanted to get some input from people on this forum.
Example:
I want to align this:
agcgaguaaaagacu
against this:
ccucuuuccaucuacagcccacuggcacuccaggcaccuaccuacuucaaacaagcucaa
gccaaggccuuccccuaacucugacugcuagucccacaguaacccugacagcugcugcuc
cugcuucuccugaacagauuauuguucaugcuuuauccccagaacauuuguugaacacaa
gugauaauguuacagugcagugucacacaccaagagucaucauucagacuguugccacag
aggacaucacuucuuccauaucccaagcagaacugaccgucgauagugauauucagucau
cugauuuuccugagccuccagacgcccuagaagcagacacuuucccagaugaaauucauc
acccuaagaugacuguggagccaucauuuaaugaugcucauguauccaaauucagugaccaaaauagcacagaacugaugaauaguguuauggucagaacagaagaagaaaucucugaca
ccgaccuuaaacaagaggaaucacccucugauuuagccagugcuuauguuacugaggguu
uagagucucccacuauagaagaacaaguugaucaaacaauugaugaugaaacaauacuua
ucguuccuucaccacauggcuuuauccaggcaucugauguuauagauacugaaucugucu
ugccuuugacaacacuaacagaucccauacuccaacaucaucaggaagaaucaaauauca
uuggaucauccuugggcaguccuguuucagaagauucaaaggaugucgaagauuugguaa
acugucauuagaauaauucu
What is the best tool to do this. Please keep in mind that I have a very large reference sequence so speed is critical - One of the main reasons I went with a BWT based tool to begin with.
Thank you!
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