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Old 09-04-2014, 04:17 AM   #1
Feng Tian
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Location: Beijing, China

Join Date: Sep 2014
Posts: 1
Question Using bedgraph to transcript assemble

Hello, I got some RNA-seq data in bedgraph format and I want to use it for transcript assembly but Cufflinks cannot accept bedgraph as input. So is there some ways to transform bedgraph into sam format
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Old 09-04-2014, 11:05 PM   #2
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While there are possibilities to convert the data, this is not what you are looking for.
The bedgraph format just gives you coordinates of the reference. You don't have any read sequence information in it and transcript assembly doesn't make much sense then.
Wherever you got your data from, ask for the original files that were used to generate the bedgraph file which has to be either sam/bam or fastq.
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bedgraph, cufflinks-2.2.1, sam

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