Ariel Paulson

Just a question, is there a way to run hicPCA with a pre-computed obs/exp matrix or a pre-computed pearson matrix? It would be nice to access the PCA functionality directly....

Hi, It would be very useful if APA could have an argument setting the max value for the color bar. In this case I am plotting loop regions from one...

Install ignores the provided python path

5

Hi, In my config-install.txt, the path is given to a custom python 3.7.9 installation: PREFIX = /home/apa/hic/hicpro/install BOWTIE2_PATH = /n/apps/CentOS7/install/bowtie2-2.4.2/bin/bowtie2 SAMTOOLS_PATH = /n/apps/CentOS7/install/samtools-1.9/bin/samtools R_PATH = /n/apps/CentOS7/install/r-4.0.0/bin/R PYTHON_PATH = /home/apa/hic/hiclib/python3/install/bin/python3.7 However,...

Fastq end mis-identification

1

Hi again, I just noticed that the fastq _1 vs _2 detection system is too general. If my fastq names contian the string "_1" anywhere, like "SPT399_10M_1.fastq.gz" and "SPT399_10M_2.fastq.gz", both...

straw and strawr don't dump same values

1

So I am dumping obs/exp data from a hic file with command-line 'straw' versus R library 'strawr', and I am not getting the same results. The data are very similar...

cannot configure with bamtools

6

Cloned today and found two issues with 'configure': File 'configure' line 5879 does not specify a path for the bamtools file 'api/BamReader.h', so it will never be able to figure...