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Old 02-20-2013, 10:05 AM   #1
tdelaney
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Location: Maryland

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Default Can CLC genomics read mapping files be used in Bioconductor/R and HTSeq-counts?

I have been using CLC Genomics for RNA-seq analyses. I am using the gaussian-based tests in CLC Genomics to detect differentially expressed genes but I am interested in using Bioconductor/R packages, such as DESeq. Can I use the exported bam/sam files produced from CLC's RNA-seq mapping tool in DESeq? Or do I need to use bam/sam files from another mapper such as TopHat? Additionally, can I use the bam/sam files from CLC as input into the HTSeq-count program? Thank in advance for you help.
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Old 02-20-2013, 09:07 PM   #2
Jeremy
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You can use a sorted bam file as input for HTSeq-count (assuming CLC generates a regular bam file) to get read counts per sample and then merge these into a table of read counts per gene (rows) for each sample (columns) as input for DESeq.
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