I noticed that average length of all mRNA transcripts from human (GRCh38) annotation was 90043.2 bp, which seems unusually high. The average length of mRNA should be 3-4,000 bp as I am aware.
Is there an explanation for this?
I calculated the average length from all entry records on GRCh38 RefSeq annotation for which the column 2 (feature type) information was “mRNA”. Below is the command that I used.
awk -v FS="\t" '$1!~"^#" && $3=="mRNA"{sum+=$5-$4;n++}END{print sum/n}' GCF_000001405.40_GRCh38.p14_genomic.gff
The “awk” that I’m using is mawk 1.3.4.
•
written
by
yh1126 •
1 answer
Seems like you (wrongly) calculated the average mRNA length on the genome (== including introns ) and thus not only the summed length of all the exons on a gene (== biological mRNA, == what you want or assumed you calculated)
You should sum&average the accumulated length of all the exon entries per mRNA in your file
Log in to answer this question.
-
Issue with VCF format while using Pharmcat
written by taniamahmood38 •
-
Converting .faa file into a data frame
written by Samet •
-
CNV annotation using GAIA
written by melissachua90 •
-
GTF file procession
written by storm1907 •
-
Tutorial: Calculation of TSS Scores for ATAC-seq Data
written by Sael •
-
Tutorial: Which human reference genome should I use?
written by finswimmer
