Hello,
I have asked this question before and didn't get any replies. I thought I will post it again as many others might be having similar problems.
I am working with miRNA-seq data set and I mapped them to the genome after adapter trimming. I am able to count the known miRNA reads using genome coordinates of precursor miRNA. That worked perfectly! Thanks to many of you who helped me do that.
What I am trying to do now is to get the read counts for individual mature miRNAs and star sequences. I am having hard time getting that information in a simplistic way.
Is there any way I can process the sam or bam file to get all the individual mature and star sequence counts separately? Right now, I am using IGV to view the alignment and basically counting the number of reads aligned to mature and star sequence. There got to be a much clever way to get this information.
Also, is there any way to detect isomiRs?
Any comments/suggestions are highly appreciated.
Thank you
I have asked this question before and didn't get any replies. I thought I will post it again as many others might be having similar problems.
I am working with miRNA-seq data set and I mapped them to the genome after adapter trimming. I am able to count the known miRNA reads using genome coordinates of precursor miRNA. That worked perfectly! Thanks to many of you who helped me do that.
What I am trying to do now is to get the read counts for individual mature miRNAs and star sequences. I am having hard time getting that information in a simplistic way.
Is there any way I can process the sam or bam file to get all the individual mature and star sequence counts separately? Right now, I am using IGV to view the alignment and basically counting the number of reads aligned to mature and star sequence. There got to be a much clever way to get this information.
Also, is there any way to detect isomiRs?
Any comments/suggestions are highly appreciated.
Thank you
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