Hello I have alot of bowtie2 data in plaintext files. What would be the easist way to convert that data into .bam files for tophat/cuffdiff
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Samtools, but tophat uses fastq files and cuffdiff would be useless on BAM files directly from bowtie2. -
So how would I prepare them for cuffdiff? Sorry if I come off uninformed I'm doing all this for my thesis projectOriginally posted by dpryan View PostComment
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Delete them and use tophat2 directly.Comment
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So I cant use anything from bowtie in tophat. The data is from bowtie2-alignLast edited by Milestailsprowe; 06-23-2015, 01:02 PM.Comment
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That's correct.Comment
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Well ok so thats helps the situation. All data must be aligned through tophat thenOriginally posted by dpryan View PostComment
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Well no, it just has to be an aligner that generates the tags needed by Cufflinks. STAR and BBMap are alternatives that generally outperform Tophat.Originally posted by Milestailsprowe View PostComment
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We can probably add HISAT to that list, or so my colleagues have mentioned recently.Comment
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