MikeAxtell
commented
6 years ago Thanks, I’ll look into it. Which version?
On Wed, Jan 17, 2018 at 5:14 AM Lonelyfighter notifications@github.com wrote:
Hi Dr. Axtell, I am using ShortStack these days and found it is quite amazing. But I have some questions about the mincov parameters. The questions is I think this version doesn't use rpm to determine the cluster as default. I made several tests using my data. In my case, the alignment rate of mapping reads is around 4%, for example. So I used rpm first (as default and also I made a test by setting rpm0.5) to run the program. But in the Results and Counts, I found many clusters with a rpm under 0.5. I tried to find the reason. I found in the log file:
At specified mincov of 0.5rpm with 11,880,255 placed primary reads, mincov is 6 raw alignments
And I found all the clusters have raw alignments above 6. I think this 6 is used to filter the cluster, but not the 0.5rpm for all the reads. In this case, all reads is 463,239,074.
I also ran with rpmm0.5 and I got the exactly the same result. But in the Results file, the rpm is calculated with all the reads (mapped + unmapped). Cause in my case, only 4% reads are mapped, that makes many clusters with a rpm under 0.5.
In the Test_DATA file, the mapped reads is near the total reads. So if the "raw alignments" is calculated by the mapped reads, it still works for the whole reads. But in my case, if the mapped ratio is low, that makes different. So if I used mapped reads 11,880,255, I got mincov is 6 raw alignmens. But if I used all reads 463,239,047, I got mincov is around 25. But the program used 6 to filter the cluster, not 25. Even when I use rpm0.5 as default.
So I am wandering if in this version, the program uses rpmm to filter the cluster, even the default set is rpm0.5. But I read you replies and found you recommended to use all the reads to calculate rpm. I am a little confused.
Could you please check if I am wrong?
Thanks a lot,
Xin.
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-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell
Lonelyfighter
Hi Dr. Axtell, I am using ShortStack these days and found it is quite amazing. But I have some questions about the mincov parameters. The questions is I think this version doesn't use rpm to determine the cluster as default. I made several tests using my data. In my case, the alignment rate of mapping reads is around 4%, for example. So I used rpm first (as default and also I made a test by setting rpm0.5) to run the program. But in the Results and Counts, I found many clusters with a rpm under 0.5. I tried to find the reason. I found in the log file:
At specified mincov of 0.5rpm with 11,880,255 placed primary reads, mincov is 6 raw alignments
And I found all the clusters have raw alignments above 6. I think this 6 is used to filter the cluster, but not the 0.5rpm for all the reads. In this case, all reads is 463,239,074.
I also ran with rpmm0.5 and I got the exactly the same result. But in the Results file, the rpm is calculated with all the reads (mapped + unmapped). Cause in my case, only 4% reads are mapped, that makes many clusters with a rpm under 0.5.
In the Test_DATA file, the mapped reads is near the total reads. So if the "raw alignments" is calculated by the mapped reads, it still works for the whole reads. But in my case, if the mapped ratio is low, that makes different. So if I used mapped reads 11,880,255, I got mincov is 6 raw alignmens. But if I used all reads 463,239,047, I got mincov is around 25. But the program used 6 to filter the cluster, not 25. Even when I use rpm0.5 as default.
So I am wandering if in this version, the program uses rpmm to filter the cluster, even the default set is rpm0.5. But I read you replies and found you recommended to use all the reads to calculate rpm. I am a little confused.
Could you please check if I am wrong?
Thanks a lot,
Xin.