priya_arasu

Simulating SV in PacBio reads

6

Hello I need some suggestions in simulating complex structural variants in Hifi reads file from PacBio https://downloads.pacbcloud.com/public/dataset/HG002-CpG-methylation-202202/m64011_190830_220126.hifi_reads.bam I could understand from the wiki page that SVs can be created in...

Merge vcf

2

Hello I tried to merge 3 vcf data sets. I get this message:  Thank you

Hello To get the correct coordinates in the bed file, what is the minimum and maximum size to be specified in the code. The vcf dataset has structural variants, each...

Run the aligned files from different smrtcells

3

Hello I need a suggestion on running the structural variant calling on hifi data from two SMRT cells. I have two aligned bam files from same subject (run in 2...

Error in executing the svafotate_main python script

2

Hello, I have been running svafotate analysis without any error. Now, I get an error when I run the svafotate script. Please find the below script used. I tried to...

I have query in the LGL simulation file, which is in the project folder. In line 24, it has been commented as "pick at random from TRUE, FALSE and original...

Installation-help

8

Hello, I am trying to install kage. Due to conflicts with packages, I am not able to install it. I first created a conda environment and installed python version 3.8...

Hello, I require some suggestions to compare the differences in protein expression between 2 conditions (P vs C). I have 3 bio-replicates and 2 conditions. Please find the snapshot. I...