illumina smallRNA adapter sequence for downstram analysis + miRNA analysis steps

[ndeshpan]

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.

Also..as 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..

cheers,

Nandan

[NicoBxl]

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)

N.

[ndeshpan]

Thanks NicoBxl,

I will use this now..

cheers

Nandan