I am a newbie in STAR. my questions:
Do you use STAR for mapping miRNA?
can you share the command lines that you use to map miRNA sequence to mirbase or genome?
Why not use bowtie v.1 (fast, ungapped alignments) which may be more appropriate in this case.
thanks! do you have best options for mirna mapping with bowtie?
Most RNA-seq tools aren't really designed for very short sequences that you get from small RNA-seq. You should look into miRNA-specific tools, such as:
miRge link does not work
Thanks for reporting. I guess things change in 3 years. Now fixed.
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