Question: How to extract un annotated (With abundant) small RNA transcript?
gravatar for barrypraveen
8 days ago by
barrypraveen10 wrote:

Hi, I have sequenced file and known small and non-coding RNA bed files. Is it possible to get unannotated with abundant small RNA transcript from my sequencing file?

sequencing rna-seq assembly • 79 views
ADD COMMENTlink modified 8 days ago by geek_y8.8k • written 8 days ago by barrypraveen10

a snippet of your files is missing.

ADD REPLYlink written 8 days ago by Pierre Lindenbaum116k

Sorry for the inconvenience, not able to add snippet. But I can explain. I have BAM and certain small RNA BED files with me. I am screening manually by IGV. My question is it possible to identify the unannotated transcript coordinates or something etc?

ADD REPLYlink written 8 days ago by barrypraveen10
gravatar for geek_y
8 days ago by
geek_y8.8k wrote:

Just convert your BED file to SAF and use FeatureCounts to quantify your BAM file over the features of your interest. Make sure your "BED" regions are not repeats or blacklisted on ucsc browser.

If you dont have coordinates of "unannotated" region, bin the genome into "n"KB bins and quantify your BAM file. This is been implemented as CSAW. Once your have the abundance from CSAW, intersect them with all known annotations and get the unannotated regions that show higher signal.

ADD COMMENTlink written 8 days ago by geek_y8.8k
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