Number of Mapped reads

[ninad]

Hi all,

I want to count the total number of mapped reads onto the reference genome.
I have .sai and .sam files. Which of these files can be used to do so?
I have low computing power, thus currently using only bwa and samtools. Please suggest me some tool to count number of mapped/unmapped reads after I align all the reads to reference genome.

Best,

[aggp11]

Hello ninad,

A quick way to do this is to first convert your sam file to a bam file. You can do this using samtools (check their documentation).

After that you can use the following command to see how many of your total reads mapped to the reference:

samtools flagstat bam_file

Hope this helps.

Praful

[vishnuamaram]

Hi ninad,

to check the no. of mapped reads, you first sort your bam file,followed by index using samtools index

then you can use.

samtools flagstat

&
samtools idxstats on your sortedbam file.