Mapping miRNA on miRBase

nedoluzhko · 09-04-2012, 02:59 AM

Hello, all! I have mapped my SOLiD reads on miRBase 19.0 (after trimming adapter, r/tRNA filtration and quality control) and found few animal and virus miRNA families in mine data. It is normal? One of these animal families is very dominant among all.

nedoluzhko · 09-05-2012, 07:22 AM

up this thread

nedoluzhko · 09-06-2012, 09:17 PM

UP. Any Answer?

NicoBxl · 09-06-2012, 11:34 PM

hey slow. let us time to answer.

So what are you type of library ? it's solid reads but did you use a special kit for small RNA ? whicj type of aligner did you use ? explain a little bit more of your workflow please.

nedoluzhko · 09-06-2012, 11:44 PM

Yes, I used SOLiD Total RNA Seq Kit (small RNA protocol), before I have conducted miRVanna enrichment. I am working with plant species without reference genom, unfortunately

Matching:

1. Preparation reads for analysis: Quality value control (SOLiD double-coded color reads with quality more than 15 were used); trimming of P2-adapter by Cutadapt program; filtration of ribosomal RNA using SILVA database and transfer RNA using Genomic tRNA database.
2. Bowtie 0.12.5 program. We mapped our 25 bp SOLiD reads on reference sequences from mirBase19.0. We used whole mirBase 19.0 for mapping with the allowance of 2-nt mismatch.
3. Generation of conservative miRNA list was conducted SAM files analysis script

NicoBxl · 09-06-2012, 11:55 PM

Did you try with an another alignment tool ? like blast ? bowtie is good to align small reads against a big reference sequence (like a genome) not small sequences.

And yes it can be normal to find some miRNA from other species. miRNA like mRNA are well conserved across species.

nedoluzhko · 09-06-2012, 11:56 PM

So, I will try! Many thanks for your help!

vtosha · 09-07-2012, 04:49 AM

Попробуйте для обработки miRDeep2, хорошая програмка. Ей можно скормить в качестве референсного любой близкий полный геном или даже просто имеющийся набор генов, она проведёт ряд фильтраций хитов по качеству и выдаст те микроРНК, что считает наиболее надёжными.

Try miRDeep2, software for searching miRNA in NGS reads. It can use as reference whole genome or set of genes, filtrate hits by quality and give out a most reliable miRNA.

nedoluzhko · 09-07-2012, 04:59 AM

Спасибо, Бласт, имхо, вообще не в тему.

Thank you!

vtosha · 09-07-2012, 05:23 AM

Если вопрос в том, может ли быть так, что среди растительных микроРНК встречаются животные, то, по-моему, может (http://www.plantcell.org/content/18/12/3355.short). Более свежих примеров навскидку не назову, но, кажется, такие есть.

If your first question was about if animal and viral microRNA was in your plant - it is possible (for example http://www.plantcell.org/content/18/12/3355.short).

nedoluzhko · 09-10-2012, 03:47 AM

Best! Thank you!

vtosha · 09-16-2012, 01:25 AM

I made a thread in Russian-language forum (http://molbiol.ru/forums/index.php?s...st=0&p=1348106) about microRNA, may be it will be useful for russian-speaking users.

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09-04-2012, 02:59 AM	#1
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	Mapping miRNA on miRBase Hello, all! I have mapped my SOLiD reads on miRBase 19.0 (after trimming adapter, r/tRNA filtration and quality control) and found few animal and virus miRNA families in mine data. It is normal? One of these animal families is very dominant among all.

09-07-2012, 04:49 AM	#8
vtosha Member Location: Moscow Join Date: May 2010 Posts: 36	Попробуйте для обработки miRDeep2, хорошая програмка. Ей можно скормить в качестве референсного любой близкий полный геном или даже просто имеющийся набор генов, она проведёт ряд фильтраций хитов по качеству и выдаст те микроРНК, что считает наиболее надёжными. Try miRDeep2, software for searching miRNA in NGS reads. It can use as reference whole genome or set of genes, filtrate hits by quality and give out a most reliable miRNA. Last edited by vtosha; 09-07-2012 at 04:53 AM.

09-05-2012, 07:22 AM	#2
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	up this thread

09-06-2012, 09:17 PM	#3
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	UP. Any Answer?

09-06-2012, 11:34 PM	#4
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	hey slow. let us time to answer. So what are you type of library ? it's solid reads but did you use a special kit for small RNA ? whicj type of aligner did you use ? explain a little bit more of your workflow please.

09-06-2012, 11:44 PM	#5
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	Yes, I used SOLiD Total RNA Seq Kit (small RNA protocol), before I have conducted miRVanna enrichment. I am working with plant species without reference genom, unfortunately Matching: 1. Preparation reads for analysis: Quality value control (SOLiD double-coded color reads with quality more than 15 were used); trimming of P2-adapter by Cutadapt program; filtration of ribosomal RNA using SILVA database and transfer RNA using Genomic tRNA database. 2. Bowtie 0.12.5 program. We mapped our 25 bp SOLiD reads on reference sequences from mirBase19.0. We used whole mirBase 19.0 for mapping with the allowance of 2-nt mismatch. 3. Generation of conservative miRNA list was conducted SAM files analysis script

09-06-2012, 11:55 PM	#6
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	Did you try with an another alignment tool ? like blast ? bowtie is good to align small reads against a big reference sequence (like a genome) not small sequences. And yes it can be normal to find some miRNA from other species. miRNA like mRNA are well conserved across species.

09-06-2012, 11:56 PM	#7
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	So, I will try! Many thanks for your help!

09-07-2012, 04:59 AM	#9
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	Спасибо, Бласт, имхо, вообще не в тему. Thank you!

09-07-2012, 05:23 AM	#10
vtosha Member Location: Moscow Join Date: May 2010 Posts: 36	Если вопрос в том, может ли быть так, что среди растительных микроРНК встречаются животные, то, по-моему, может (http://www.plantcell.org/content/18/12/3355.short). Более свежих примеров навскидку не назову, но, кажется, такие есть. If your first question was about if animal and viral microRNA was in your plant - it is possible (for example http://www.plantcell.org/content/18/12/3355.short).

09-10-2012, 03:47 AM	#11
nedoluzhko Member Location: Russia, Moscow Join Date: Aug 2009 Posts: 22	Best! Thank you!

09-16-2012, 01:25 AM	#12
vtosha Member Location: Moscow Join Date: May 2010 Posts: 36	I made a thread in Russian-language forum (http://molbiol.ru/forums/index.php?s...st=0&p=1348106) about microRNA, may be it will be useful for russian-speaking users.