Question: Rna-Seq Tag Count
1
gravatar for Rna-Seq
8.7 years ago by
Rna-Seq50
Japan
Rna-Seq50 wrote:

Hi,

I've RNA-seq illumina data and i would like to find differentially expressed genes,I mapped the data and now i should write a script for tag counting. I wonder is there a ready made function for tag counting that i can use or i have to write my own script..

Thank you in advance and Best Regards.

rna • 3.3k views
ADD COMMENTlink written 8.7 years ago by Rna-Seq50
3
gravatar for Vitis
8.7 years ago by
Vitis2.3k
New York
Vitis2.3k wrote:

HTSeq package does that, it's based on python. It takes a gff3 as part of the input to define tags. Also, R package IRanges has a function called countOverlap, which also does the same thing, counting reads mapped to defined tags. Here, you may use a gff3 as input, convert it into a Granges object and count overlapped reads on top of that. I'd recommend the HTSeq solution if your bam/sam files are very large, as R tends to take the entire alignment at once. If you don't have a huge memory, you're out of luck.

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Vitis2.3k

I think HTSeq-count is a superior soultion to countOverlap because it has options to deal different ambiguities scenarios one would have to code oneself.

ADD REPLYlink written 8.7 years ago by Ido Tamir5.0k
2
gravatar for Marina Manrique
8.7 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

Have you tried Cufflinks? It's pretty straightforward

http://cufflinks.cbcb.umd.edu/

ADD COMMENTlink written 8.7 years ago by Marina Manrique1.3k
0
gravatar for Travis
8.7 years ago by
Travis2.8k
USA
Travis2.8k wrote:

You could also look up RUM (RNASeq Unified Mapper) as a complete mapping/counting solution for Illumina data.

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Travis2.8k

edgeR, DESeq, NOISeq don't do tag counting, but take as input a tag counted file.

ADD REPLYlink written 8.7 years ago by Ido Tamir5.0k

Comment edited, thanks.

ADD REPLYlink written 8.7 years ago by Travis2.8k
0
gravatar for Madelaine Gogol
8.7 years ago by
Madelaine Gogol5.1k
Kansas City
Madelaine Gogol5.1k wrote:

coverageBed from bedtools can do it too.

ADD COMMENTlink written 8.7 years ago by Madelaine Gogol5.1k
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