read count

[cmccabe]

Using samtools view <BAM> chr:532155-532310 I get 2410 reads and in IGV I get many more reads.  Is there:

 

1. a way to export the total reads of a region in IGV

2. why is the read count less using samtools

3. Is IGV looking at the data in a different way

 

I am rather new to next gen data so I am trying to understand.  Thank you. 

[Jim Robinson]

Hi,

You can't export from IGV at the current time, but you can run "igvtools" from the command line to do a count over a region.   For the output file use a ".wig" extension to get a text wig file, rather than the default binary tdf file.  See the igvtools documentation for more details.

I can't really say what samtools is doing.  IGV is just counting how many reads overlap each locus,  really as raw and basic a count as you can do.

Jim