i am very new to bioinformatics and been trying to learn new things every day.
this time, i need to find out RPKM from a sam file. i mapped RNAseq reads to refMrna and have a sam file generated. the data was single end and had length 36. from the sam file, i took the number of unique counts of all genes that were mapped. now i have a count file with gene name and its count.
eg.
NM_000172 31239
NM_000242 26765
NM_000265 5160
NM_000267 28499
NM_000356 27352
the RPKM formula suggests..
(number of reads mapped to a gene/ (totat number of reads X read length)) X 10^9
so, for the first read mapped, NM_000172, the number of reads mapped is 31239, read length is 36.
but what will be the total number of reads ?? is it all the reads that were mapped in sam file. including flags like *
please guide
this time, i need to find out RPKM from a sam file. i mapped RNAseq reads to refMrna and have a sam file generated. the data was single end and had length 36. from the sam file, i took the number of unique counts of all genes that were mapped. now i have a count file with gene name and its count.
eg.
NM_000172 31239
NM_000242 26765
NM_000265 5160
NM_000267 28499
NM_000356 27352
the RPKM formula suggests..
(number of reads mapped to a gene/ (totat number of reads X read length)) X 10^9
so, for the first read mapped, NM_000172, the number of reads mapped is 31239, read length is 36.
but what will be the total number of reads ?? is it all the reads that were mapped in sam file. including flags like *
please guide
Comment