Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
trim adapter from Illumina Genome Analyzer IIe miRNA reads NicoBxl Bioinformatics 5 01-02-2014 06:31 AM
miRNA identification in plants using smallRNA deep SEQ data PRJ Bioinformatics 4 09-13-2013 05:11 AM
PubMed: Initial steps towards a production platform for DNA sequence analysis on the Newsbot! Literature Watch 0 03-09-2011 11:40 AM
SmallRNA analysis pipeline naluru SOLiD 5 12-13-2010 12:59 AM
In Sequence: With GenomeStudio, Illumina Adds Analysis Software Tools for Its Genome Newsbot! Illumina/Solexa 0 10-21-2008 01:15 PM

Thread Tools
Old 06-09-2011, 11:42 PM   #1
Location: Sydney

Join Date: Nov 2009
Posts: 29
Default illumina smallRNA adapter sequence for downstram analysis + miRNA analysis steps

Hi all,

I have got two data-sets (36 bp) illumina reads from a smallRNA experiment.

Can anyone tell me what specific adapter sequence (sequence in ACGT) needs to be provided to the miRNA analysis tools such as novoalign/mirExpress etc for removing these adapters before alignment. per my search from seqanswers and other sources..the pipeline I need to use for general expression profiling between two sets of reads looks something like this...

1) Adapter trimming and quality filtering
2) Mapping against mirBase to separate out known /novel miRNAs
followed by
3) miRNA abundance profiling?
Any suggestions as to what is the best tool for this step?

Did I miss any steps?

appreciate any replies..


ndeshpan is offline   Reply With Quote
Old 06-10-2011, 12:58 AM   #2
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264

for the adapter check in the Genome Analyzer II topic.

It would be a good idea to map your reads on your reference genome before to map them on mirbase. You can use bowtie to align the reads against the genome and IGV to visualize the alignment ( bowtie output is in sam format. You've to convert it to bam file before loaded it in IGV )

For abundance profiling: check DESeq or edgeR (two bioconductor R packages)

NicoBxl is offline   Reply With Quote
Old 06-14-2011, 10:44 PM   #3
Location: Sydney

Join Date: Nov 2009
Posts: 29

Thanks NicoBxl,

I will use this now..


ndeshpan is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:33 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO