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Old 12-08-2011, 02:03 PM   #1
koneru_18
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Location: United States

Join Date: Oct 2011
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Default Resources for miRNA Expression

Hello,

I have miRNA expression data of control and disease samples. What are the resources to identify differential expression in the miRNA samples?

Can someone help me on this?

Thanks in advance
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Old 12-12-2011, 12:38 AM   #2
sudders
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Hi Koneru,

A simple first thing to try might be to count the number of reads that map over each microRNA on the genome and just use DESeq or EdgeR to test for differential expression.

We count overlaps with genomic regions using the coverageBED program which is part of the bedtools package.

A sample work flow might be:

1) Map miRNA reads to the genome with Bowtie
2) You can get a gtf with the genomic co-ordinates of miRNAs from miRBase.org, convert it to a BED.
3) Run coverageBED using the bed file you generated in 2 and the bam file from Bowtie
4) Repeat for each of your samples
5) Use DESeq to test for differential expression between your samples.

Ian
---
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Old 12-23-2011, 08:57 PM   #3
polsum
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Location: Texas

Join Date: May 2009
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Quote:
Originally Posted by sudders View Post
Hi Koneru,

A simple first thing to try might be to count the number of reads that map over each microRNA on the genome and just use DESeq or EdgeR to test for differential expression.

We count overlaps with genomic regions using the coverageBED program which is part of the bedtools package.

A sample work flow might be:

1) Map miRNA reads to the genome with Bowtie
2) You can get a gtf with the genomic co-ordinates of miRNAs from miRBase.org, convert it to a BED.
3) Run coverageBED using the bed file you generated in 2 and the bam file from Bowtie
4) Repeat for each of your samples
5) Use DESeq to test for differential expression between your samples.

Ian
---
How do you account for multiple mappings? if a read maps on more than 1 genomic location, how do you assign the read to different mappings? thanks.
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Old 10-15-2013, 05:05 AM   #4
unique379
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Location: Italy

Join Date: Aug 2012
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hello all,

I would like to have Genome coordinates of miRNAs in .gtf (miRNA.gtf) format so, is it possible to convert from .gff3 from miRBase ?? if yes the how ??


Thanks and looking forward for your kind reply
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