MiRBase miRNA analysis with STAR

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3.3 years ago

Nitish Mishra ▴ 30

Hi All,

I am using the latest mice reference genome (GRCm39) for small RNAseq/miRNA-seq analysis. MiRBase database doesn't have any GFF/GTF file for the mouse mature-miRNA/loop-miRNA.

I just have mature-miRNA and loop-miRNA fasta sequences from MiRBase. How I can use the STAR tool to generate genome index and GeneCounts by using fasta miRNA fasta file? I want use STAR for generating read counts for each miRNA by using --quantMode TranscriptomeSAM GeneCounts.

Thanks

miRNA GRCm39 MiRBase STAR • 2.5k views

ADD COMMENT • link 3.3 years ago by Nitish Mishra ▴ 30

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How about using a dedicated workflow that is meant to this type of analysis. STAR is not the best tool for aligning small RNA's with a genomic reference.

ADD REPLY • link 3.3 years ago by GenoMax 147k

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Thanks GenoMax , smranaseq tool will use miRBase gff3 in the background. Currently, the miRBase gff3 link is not working so it will not work.

Secondly, even if it will work, it still not going to work with mm39, as miRBase gff3 is for the previous version of the reference genome (mm38).

STAR will work for miRNA genes but not for the mature miRNA as suggested by ENCODE.

I will use bowtie1 and samtools view for the mature miRNA.

ADD REPLY • link 3.3 years ago by Nitish Mishra ▴ 30

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