I have been using bowtie2 to align my reads to an indexed reference genome and used the --un-conc and --al-conc functions to separate out the aligned and non aligned reads into separate files, however I have just received a new data set which has been merged. I have tried using the -U option in bowtie2 to see if this worked but it doesn't seem to. Does anyone know of another program I could use for this and the appropriate command? I am looking into BWA to see if this is an option but am new to the program.
Thanks,
Tom
Thanks,
Tom
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