miRNA-seq

FKrys

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Join Date: May 2014

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miRNA-seq

05-29-2014, 06:49 AM

Hi!!!
I'm new with NGS analysis and I have a problem with miRNA data (Illumina, 4 cell types, 3 replicates, 12 samples). I'm using galaxy. First I removed adapters and abundant sequence using fastQC and trim galore. Subsequently I aligned my FASTQ file with contaminant.fa using Bowtie2 and considering the unaligned reads for the next steps. Then I align these to mature.fa and precursor.fa, both taken from iGenomes (small RNA- mm10). For the alignment to the genome sequences I consider trimmed reads and align against the genome mm10 (Bowtie2Index). Can anyone tell me how to proceed with the analysis?
thank you very much
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