Question

How to extract un annotated (With abundant) small RNA transcript?

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5.3 years ago

PK ▴ 130

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?

RNA-Seq sequencing Assembly • 1.0k views

ADD COMMENT • link updated 5.3 years ago by GouthamAtla 12k • written 5.3 years ago by PK ▴ 130

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a snippet of your files is missing.

ADD REPLY • link 5.3 years ago by Pierre Lindenbaum 161k

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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 REPLY • link 5.3 years ago by PK ▴ 130

score 1 · Answer 1 · 2019-01-10

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.