Samantha Klasfeld
Samantha Klasfeld
### set seed for biostar145820.jar I am using biostar145820.jar to subsample bam files, and it works great. I was just wondering if there is a seed in the random shuffle...
To call peaks from multiple replicates I first extended the reads, normalized the signal in each replicate, and then took the average signal at each base pair using my own...
**Use case** I had 20 different bam files from different publications (so some have different read-sizes) and I ran MACS2 with them. For the code below I will just refer...
I am running MACS2 and I wanted to see which regions were called without extended the reads towards the 3' end. Therefore, I set --nomodel and --extsize 0 (since by...
Hello, I tried using --genomebam to visualize the reads mapped from a genome perspective. I also input the gtf and chromosome files. The bam files contain flags that say whether...
when I run the following: `so
Good afternoon, I downloaded the [358 input bam files](https://github.com/Boyle-Lab/Blacklist/tree/master/lists/metadata) for Drosophila (dm3). Next I downloaded the respective [umap files](http://ftp.encodedcc.org/modENCODE_VS_ENCODE/Regulation/Fly/mappability/). Then I ran the blacklisting tool. It did not give me...
Hello, I was just wonder how MACS2 deals with unequal treatments and controls. For example, if I have three input replicates, does it make sense to use them all even...
When the user changes the experiment view screen to be smaller, the buttons at the top of the main table should not interfere with the table below it. These changes...