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I am using bowtie and have been outputting .bwt files but now need to convert those files to .sam format. I know bowtie has a .sam output option (-S) which I am now using, however I need to convert all the files I have produced so far using the .bwt format into SAM files so I don't lose all the work I have done so far. Using bowtie2sam.pl I can easily convert the files but the new files don't have headers, which is I need for the SAM -> BAM conversion. Is there a way to convert the files that creates headers or would it be better to manually add new headers with a loop of some kind? Thanks for the help!
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