miRNA filtration question
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Hello again,
This is a question rather than an issue. Could you please explain what the difference between the columns "All.miRNA.Reads" and "Filtered.miRNA.Reads"? I can't find any documentation on any filtering procedures except for isomer identification and this run was performed without that flag so I don't know what filtering procedures are being applied.
Thank you!
Hi @Glfrey,
The All.miRNA.Reads counts points to reads that map to both canonnical and isomiRs (mapped.csv). There are two filters we have in place here, as explained below for Filtered.miRNA.Reads:
- If canonical reads (first column with strict allignment) has < two hits, then the hit is replaced with zero in both canonical and isomiRs (last column). This will eliminate very small fraction of noise.
- The second is the option of
--crThresholdi.e., the threshold of the proportion of canonical reads for the miRNAs to retain. Range for ex (0 - 0.5), (Default: 0.1). The number of reads mapping to canonnical over isomirs should be > 0.1, any read counts with ratio less than specified will be removed by default.
These above filtering make up the revised All.miRNA.Reads, now known as Filtered.miRNA.Reads. I hope I have not missed anything, @mhalushka, can suggest/confirm.
Thank you,
Arun.