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Hi,I have a question ,I used illumina single-end 32mer read to ran tophat on galaxy,and then use hit.bam ran cufflink but fail(error).Does anyone know can cufflink run sinle-end reads? Thanks!
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Maybe the cufflinks can't read the bam files. I remember that cuffllinks need sam files as its input.Change bam file to sam file with samtool and have another try. -
Originally posted by feixue1039 View Post
But in my other case,I ran paired-end read in tophat,and also use hit.bam to run cufflink is OK.
Therefore,I guest cufflink on galaxy's parameters, not apply to single-end readsComment
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THanks,Everyone,I know the ansewr.Your hit.bam need to edit source of database:hg19.Comment
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