Hi,
I'm getting a very low proportion of miRNAs in my small RNA-Seq samples.
At least, I think the proportion of miRNAs is very low.
I always get less than 2.5% of miRNAs in all my samples, using the Illumina small RNA sample prep kit.
Would you consider this low?
Are you getting higher proportions?
If so, what what proportions are you getting and which protocols are you using?
The reads do align on the reference genome, after trimming.
There seems to be a lot of tRNA.
The RA3 adapter was removed with Cutadapt.
The miRNA analysis was done with Cap-mirSeq and mirDeep2.
Bowtie log:
# reads processed: 31242819
# reads with at least one reported alignment: 26293368 (84.16%)
# reads that failed to align: 3855506 (12.34%)
# reads with alignments suppressed due to -m: 1093945 (3.50%)
Reported 37407783 alignments to 1 output stream(s)
mirDeep2 log of reads aligning directly on miRBase
# reads processed: 1002221
# reads with at least one reported alignment: 22340 (2.23%)
# reads that failed to align: 979881 (97.77%)
Incidentally, I have more knowledge in bioinformatics than in library preparation but I will discuss with our molecular biology platform any useful information you could give me.
Thank you for your help.
I'm getting a very low proportion of miRNAs in my small RNA-Seq samples.
At least, I think the proportion of miRNAs is very low.
I always get less than 2.5% of miRNAs in all my samples, using the Illumina small RNA sample prep kit.
Would you consider this low?
Are you getting higher proportions?
If so, what what proportions are you getting and which protocols are you using?
The reads do align on the reference genome, after trimming.
There seems to be a lot of tRNA.
The RA3 adapter was removed with Cutadapt.
The miRNA analysis was done with Cap-mirSeq and mirDeep2.
Bowtie log:
# reads processed: 31242819
# reads with at least one reported alignment: 26293368 (84.16%)
# reads that failed to align: 3855506 (12.34%)
# reads with alignments suppressed due to -m: 1093945 (3.50%)
Reported 37407783 alignments to 1 output stream(s)
mirDeep2 log of reads aligning directly on miRBase
# reads processed: 1002221
# reads with at least one reported alignment: 22340 (2.23%)
# reads that failed to align: 979881 (97.77%)
Incidentally, I have more knowledge in bioinformatics than in library preparation but I will discuss with our molecular biology platform any useful information you could give me.
Thank you for your help.
Comment