MAQ and small RNAs

danielsbrewer · 02-24-2009, 07:22 AM

Hi,

I am new to analysing next generation sequencing data but have recently got involved in a Solexa project that aims to detect differences in small RNAs between tumour and normal samples. I have the resulting fastq read files which have had the adapter removed.

What I would like to know is the best settings to use with maq map for this kind of analysis.

1) I need to have a cut-off on the size of the reads used. I think you would use something like "-1 15" to only look at reads above 15 length
2) I think it is normal to allow a mismatch of 2 ... is this ok for small RNA stuff?
3) Anything else I need to look at?

One thing I can't understand is that even when I had the mismatch setting set at 2 the number of mismatches for the best match for some of the reads were way above that even getting up to 6.

Lastly is there any good resources for MAQ and small RNAs?

Many Thanks

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
study design small RNAs	Conny	Sample Prep / Library Generation	5	11-11-2011 06:47 AM
PubMed: Large-scale sequencing of plant small RNAs.	Newsbot!	Literature Watch	0	08-07-2011 06:12 AM
DEGseq and expression of novel small RNAs	mgolo	RNA Sequencing	0	07-19-2011 07:28 AM
Grouping small RNAs for analysis	DrD2009	Bioinformatics	8	09-01-2010 01:18 PM
How to present the nucleotide bias of small RNAs using weblogo	satp	Bioinformatics	0	02-10-2010 12:51 AM

02-24-2009, 07:22 AM	#1
danielsbrewer Member Location: UK Join Date: Feb 2009 Posts: 33	MAQ and small RNAs Hi, I am new to analysing next generation sequencing data but have recently got involved in a Solexa project that aims to detect differences in small RNAs between tumour and normal samples. I have the resulting fastq read files which have had the adapter removed. What I would like to know is the best settings to use with maq map for this kind of analysis. 1) I need to have a cut-off on the size of the reads used. I think you would use something like "-1 15" to only look at reads above 15 length 2) I think it is normal to allow a mismatch of 2 ... is this ok for small RNA stuff? 3) Anything else I need to look at? One thing I can't understand is that even when I had the mismatch setting set at 2 the number of mismatches for the best match for some of the reads were way above that even getting up to 6. Lastly is there any good resources for MAQ and small RNAs? Many Thanks