These are chat archives for dereneaton/ipyrad

7th
Feb 2017
Isaac Overcast
@isaacovercast
Feb 07 2017 18:39
@LinaValencia85 For SE mapped and unmapped reads should be accurate. For PE samtools counts both R1 and R2 as "reads" so when it reports "mapped reads" it's double-counting (at least compared to ipyrad where all the other stats we report count R1+R2 as one read). If you have PE you can divide the ipyrad reported mapped and unmapped reads by 2 and this should be accurate.
@amelymartins Can you give me an example of how the output of samtools flagstat and the stats from s7 aren't matching? Internal to ipyrad I'm literally running samtools flagstat and grabbing the results for the stats files, so i'm a little at a loss for what could be happening.