SOLID reads

EADIE · 08-22-2010, 02:05 AM

hi,
i wonder to know what should i do before mapping reads to reference genome?
reads is like:
>853_1434_503_F3
T00010230120200223112313302010303131
>853_1434_640_F3
T10110321132100321101032203211113333
>853_1434_723_F3
T10002311323331221330201030303112312
>853_1434_796_F3
T33330210031203013231322323302010303
>853_1434_1327_F3
T11231011321333211013021301000330201
these reads are for microRNA analysis, while as we known, microRNA's length is approximate 20nt, my reads are 35bp, should i shorten them?

jjohnson · 08-22-2010, 08:57 AM

Hi EADIE,

I think it depends on how you intend on processing the data. Software like bioscope and CLCBio will dynamically trim your data to remove adapters and non-miRNA sequence. They both also (in different ways) can help you annotate known miRNA against MIRBASE or other annotation sources. Handling this data like traditional re-sequencing data using mapping software such as bfast, bowtie, bwa, CLC, etc will probably not provide you with the results you are looking for. Happy to help more if needed.

EADIE · 08-25-2010, 02:23 AM

Quote:

Originally Posted by jjohnson

Hi EADIE,

I think it depends on how you intend on processing the data. Software like bioscope and CLCBio will dynamically trim your data to remove adapters and non-miRNA sequence. They both also (in different ways) can help you annotate known miRNA against MIRBASE or other annotation sources. Handling this data like traditional re-sequencing data using mapping software such as bfast, bowtie, bwa, CLC, etc will probably not provide you with the results you are looking for. Happy to help more if needed.

thanks for your reply! it helps me a lot...
does bioscope or CLCBio is free? or should i write a perl script to remove adapters? is there any other free tools to do that?

jjohnson · 08-25-2010, 06:51 AM

RNA2MAP, which is part of the SOLiD open source software community is free to use: http://solidsoftwaretools.com/gf/project/rna2map/

CLC is a commercial package, but you can get a 2 week demo: http://www.clcbio.com

EADIE · 08-28-2010, 12:19 AM

Quote:

Originally Posted by jjohnson

RNA2MAP, which is part of the SOLiD open source software community is free to use: http://solidsoftwaretools.com/gf/project/rna2map/

CLC is a commercial package, but you can get a 2 week demo: http://www.clcbio.com

can RNA2MAP have the function of removing adapters and producing data of csfasta format?
bother you again...

westerman · 08-30-2010, 02:05 PM

Quote:

Originally Posted by EADIE

can RNA2MAP have the function of removing adapters and producing data of csfasta format?
bother you again...

No. The manual does not mention generating csfasta file as the 6 possible outputs.

Since the documentation is free and available you could take a quick look at it and see if the program mets your needs.

toni_marco · 12-12-2011, 07:39 AM

Hi,

We just published a paper on microRNA detection using color space. I think that may be of your interest. We discuss how to efficiently remove adaptors and show why SOLiD RNA2MAP may be problematic to detect multiple-copy microRNAs. An advance access of the paper is just available from Bioinformatics site.

http://bioinformatics.oxfordjournals...tr686.abstract

Cheers,
Toni

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
bowtie for SOLiD reads	holywoool	Bioinformatics	0	09-14-2011 07:39 PM
Mapping of SOLiD reads	JohanS	SOLiD	2	05-26-2011 04:04 AM
BFAST solid reads	newbietonextgen	Bioinformatics	1	01-26-2011 08:36 PM
Filtering SOLiD reads	k-gun12	Bioinformatics	8	03-12-2010 09:51 PM
Alignment of ABI solid reads and 454 reads	baohua100	Bioinformatics	2	02-23-2009 05:58 PM

08-22-2010, 02:05 AM	#1
EADIE Member Location: CHINA Join Date: Mar 2010 Posts: 11	SOLID reads hi, i wonder to know what should i do before mapping reads to reference genome? reads is like: >853_1434_503_F3 T00010230120200223112313302010303131 >853_1434_640_F3 T10110321132100321101032203211113333 >853_1434_723_F3 T10002311323331221330201030303112312 >853_1434_796_F3 T33330210031203013231322323302010303 >853_1434_1327_F3 T11231011321333211013021301000330201 these reads are for microRNA analysis, while as we known, microRNA's length is approximate 20nt, my reads are 35bp, should i shorten them?

08-22-2010, 08:57 AM	#2
jjohnson Member Location: Washington DC Metro Area Join Date: Aug 2009 Posts: 20	Hi EADIE, I think it depends on how you intend on processing the data. Software like bioscope and CLCBio will dynamically trim your data to remove adapters and non-miRNA sequence. They both also (in different ways) can help you annotate known miRNA against MIRBASE or other annotation sources. Handling this data like traditional re-sequencing data using mapping software such as bfast, bowtie, bwa, CLC, etc will probably not provide you with the results you are looking for. Happy to help more if needed. __________________ Justin H. Johnson \| Twitter: @BioInfo \| LinkedIn: http://bit.ly/LIJHJ \| EdgeBio

08-25-2010, 06:51 AM	#4
jjohnson Member Location: Washington DC Metro Area Join Date: Aug 2009 Posts: 20	RNA2MAP, which is part of the SOLiD open source software community is free to use: http://solidsoftwaretools.com/gf/project/rna2map/ CLC is a commercial package, but you can get a 2 week demo: http://www.clcbio.com __________________ Justin H. Johnson \| Twitter: @BioInfo \| LinkedIn: http://bit.ly/LIJHJ \| EdgeBio

12-12-2011, 07:39 AM	#7
toni_marco Junior Member Location: Manchetser, UK Join Date: Nov 2009 Posts: 5	Detection of microRNAs in color-space Hi, We just published a paper on microRNA detection using color space. I think that may be of your interest. We discuss how to efficiently remove adaptors and show why SOLiD RNA2MAP may be problematic to detect multiple-copy microRNAs. An advance access of the paper is just available from Bioinformatics site. http://bioinformatics.oxfordjournals...tr686.abstract Cheers, Toni