how to extract 3` utr from transcriptome

[Farbod Emami]

Dear Brian, Hi

I want to create a 3` UTR database of my de novo RNA-seq Trinity assembly to use it as a source for target prediction for miRNAs using Miranda algorithm.

Is there any way to extract 3` utr from transcriptome of a non-model species?

Thanks

[thileepan sekaran]

Hi farbood Emani,

With grep function which I advised, you could generate a bed file like following

grep "three_prime_UTR" your_gff3 > output_3_prime_UTR.bed".

Later you can make use of  bedtools getfasta like following

bedtools getFasta -fi your_fasta_file -bed output_3_prime_UTR.bed -fo output.fasta

On Tue, Apr 12, 2016 at 12:22 PM, Farbod Emami <farbo...@gmail.com> wrote:

Dear thileepan sekaran , Hi

Thank you for your help but would you please tell me how I can extract "The Sequence" of 3 prime UTRs of my transcriptomes? as the MiRamda needs a fasta file of these 

sequences for miRNA target prediction.

Thank you in advance

On Tue, Apr 12, 2016 at 1:06 PM, thileepan sekaran <dena....@gmail.com> wrote:

Hi,

IF you have a GFF3 file generated by transdecoder for your transcriptome, you could easily make use use grep "three_prime_UTR" your_gff3 > output.txt". This command will output only the 3_prime_UTR regions(Start and End) for every transcript in your transcriptome.

Reagrds

Deena

 

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