Comments (9)
How do you calculate ribosomal RNA content?
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Hmm. I dont know. I will have to find out.
@pajailwala used in a recent project. Does he know where?
--Vishal
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Hi Parthav,
I need to double check with Maggie, but I thought she was mentioning Picard RNASeqMetrics. Don't we have the RNAseqMetrics calculated in the pipeline?
Bong-Hyun
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Yes. Bong-Hyun, it does seem to report it.
https://broadinstitute.github.io/picard/picard-metric-definitions.html#RnaSeqMetrics
--Vishal
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Yes Parthav,
Thats right. We do have RIBOSOMAL_BASES showing number of RNA bases covered in the bam file. and it is dependent on the RRNALIST provided, which generally are :
- "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19.rRNA.interval_list_v3"
- "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26" and
- "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10.rRNA.interval_list_M12".
As per picard,
RIBOSOMAL_BASES --> Number of bases in primary alignments that align to ribosomal sequence.
This to me only indicates if the rDNA bases that are covered by sequencing, but does not give any idea about the depth at these bases. I think one is going to have some coverage over these bases, no matter what. It is how often they are covered that is important to us. Isnt it?
--Vishal
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Added rRNA index in FqScreen. This close #263
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Related Issues (20)
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