Hi all,
I'm an amateur at bioinformatics, so I'm having a bit of trouble with trying to get some information out of Chip-Seq data. I would like to know if there is a way to get the sum of the amount of Chip on genes based on a list (like the tables from UCSC).
I have .bam files and .wig files, and my current solution is that I'm trying to create a JAVA program to sum up the amount based on the .wig file with the reference table, but I was wondering if there was a more efficient / accurate option.
Basically, I'm looking for gene by gene normalized sums similar to the FPKM I get from cufflinks for RNA-seq, but for Chip-seq. (Is feasible to run cufflinks on Chip-Seq data?)
Up until now I have only been able to get any sort of sums out of the wiggle files was by taking the summing the numbers from SitePro's text file with profiles, but that will only get me sums around a certain point, not for the gene bodies.
Is this clear?
Can anybody help me?
I would appreciate any assistance anyone could provide.
-BenS
I'm an amateur at bioinformatics, so I'm having a bit of trouble with trying to get some information out of Chip-Seq data. I would like to know if there is a way to get the sum of the amount of Chip on genes based on a list (like the tables from UCSC).
I have .bam files and .wig files, and my current solution is that I'm trying to create a JAVA program to sum up the amount based on the .wig file with the reference table, but I was wondering if there was a more efficient / accurate option.
Basically, I'm looking for gene by gene normalized sums similar to the FPKM I get from cufflinks for RNA-seq, but for Chip-seq. (Is feasible to run cufflinks on Chip-Seq data?)
Up until now I have only been able to get any sort of sums out of the wiggle files was by taking the summing the numbers from SitePro's text file with profiles, but that will only get me sums around a certain point, not for the gene bodies.
Is this clear?
Can anybody help me?
I would appreciate any assistance anyone could provide.
-BenS
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