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How To Putatively Identify Intronic Regions/Splice Sites Based On Sequence In Lincrna?

Hello,

I have a list of unannotated lincRNA (cf. Human Body Map, Broad Institute) and in order to make primers for these, I need to identify intronic regions. Any ideas how to putatively identify intronic regions/splice sites based on sequence in lincRNA?

Thanks.

intron
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updated by JC JC • written by Eric • Eric

When you say you have "unannotated lincRNA", what do you have? Do you have FASTA sequence, some identifiers, or something else?

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written by Sean Davis Sean Davis

FASTA sequence.

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written by Eric • Eric

2 answers

I assume, you have BED genomic co-ordinates. Then use the following script to extracts introns. 

awk '{
n11 = split($11, t11, ",")
n12 = split($12, t12, ",")
for (i = 0; ++i < n11 – 1;) {
s12 = $2 + t12[i]
print $1, s12 + t11[i], $2 + t12[i + 1], i "I_" $4
}
}' file.bed
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written by biorepine biorepine

it's unclear to me where the bed file would be input in your script.

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written by Eric • Eric

replace the $1 with your file name and also try to retype the script instead of copying as some of the characters (" , ' etc) couldn't copy well.

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written by biorepine biorepine

I have typed in the script, replacing $1 with my filename (intron.txt), but get the following:

-bash: awk{n11=split($11,t11,",") n12=split($12,t12,",") for (i=0; ++i < n11;){s12=$2+t12[i] print intron.txt,s12,s12+t11[i],i"E_"$4}}intron.txt: command not found

Perhaps I've misunderstood. Any suggestions?

I'm also curious how it identifies the introns, if you have the time.

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written by Eric • Eric

try the above updated code.

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written by biorepine biorepine

If you have the fasta sequence for each lincRNA, I will map them using blat to the reference genome, that will give you the genomic coordinates for exons/introns.

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written by JC JC

Broad Institute's put their lincRNA catalog onto the UCSC browser now, so this is certainly the easiest route. Thanks.

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written by Eric • Eric

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