Number of reads mapped to genome

Question

[vimlakany]

Hi, while calculating RPKM, how to get the number of reads mapped to genome. The total read counts is 11851490
I have tried samtools flagstat file.bam, the result is

12955438 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
12255658 + 0 mapped (94.60%:-nan%)
12955438 + 0 paired in sequencing
6477719 + 0 read1
6477719 + 0 read2
11999942 + 0 properly paired (92.62%:-nan%)
12234952 + 0 with itself and mate mapped
20706 + 0 singletons (0.16%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

from the above result
1) which value should i take for number of reads mapped to genome, while calculating RPKM.
2) The total read counts is 11851490 and how does it increase to 12955438, 12255658,

Answer 1

[Devon Ryan]

Please do samtools view -c -F 256 -f 66 file.bam and use the number it outputs as the number of fragments. You can then use that for the FPKM (not RPKM, since you have a paired-end dataset) calculation.

The reason there are more entries than original reads in the BAM file is due to secondary alignments.

As an aside, make sure you have a good reason to use RPKMs/FPKMs, since for the most part they should be avoided.

[vimlakany]

Thank you. can you please tell me the difference between 12255658 + 0 mapped (94.60%:-nan%) and 12955438 + 0 paired in sequencing

[Devon Ryan]

12955438 is the number of entries, whether aligned or not. The other number is the percent aligned.

[vimlakany]

so while calculating RPKM, will it be correct or meaningful if i take total number of reads mapped to genome as 12255658?
can you please tell me the difference between 11999942 + 0 properly paired (92.62%:-nan%) and 12234952 + 0 with itself and mate mapped.
What is the difference between mapped reads and properly paired reads?

[Devon Ryan]

Using 12255658 would yield values that are artificially small. The two numbers you referenced are for proper pairs and that plus discordant pairs (e.g., wrong relative orientation).

[Macspider]

Since you asked:

• Mapped reads are reads that found a match on the reference sequence given the allowed mismatches / indels and all other restraints that you applied

• Proper pairs are pairs of reads that both map and are within the insert size (which is a property of the sequencing library that you should know / have received with the data / have inferred by the TLEN field of the bam file resulting from the alignment of a subset of reads