Monopogen
Monopogen copied to clipboard
KChen-lab
SNV calling from single cell sequencing
Hello, Thank you for developing such a wonderful tool. Recently, I attempted to execute somatic variant calling from scRNA-seq data. The preprocess and germline calling sections executed successfully. However, I...
**Case**: using our bam file, the result of char20.germine.vcf contains nothing **Description**: To test your code, we used the same region.lst under the `./example` folder, and used our own bam...
Hello, I use single cell sequencing data to run somatic SNV calling from scRNA-seq. It takes a lot of time when I run the second step (cellScan), about 30+ hours....
When I conducted the germline calling process, I noticed that only a limited number of chromosomes were successfully processed into 'phased.vcf.gz,' whereas most of the chromosomes remained unprocessed. I included...
Hello!Thank you for developing monopogen! I run the code:**python ${path}/src/Monopogen.py preProcess -b test.lst -o 01.test -a ${path}/apps**,but got error like this: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/public/home/user/program/miniconda3/envs/monopogen/lib/python3.7/multiprocessing/pool.py",...
Hello, thank you so much for developing Monopogen. I get this error when I run the preProcess module. I tried my bam files and also the bam files you provided...
Hello all, Thank you for making this great tool. In the example, the germline caller is used for chromosome 20 only. If we wish to perform germline calling for chromosomes...
Hello, Thank you for developing such a wonderful method. Recently, I attempted to execute somatic variant calling from scRNA-seq data, following the step-by-step instructions provided on your GitHub repository. However,...
Hello, thank you for developing great software. I tried to run germline genotyping using 16 threads, but it did not work multithreading on Beagle phasing step. I think it forgets...
Hello, I've tried running Monopogen with the below parameters and run into an error where there is a ```Incorrect number of FORMAT fields at chr20:2998993 .. DP, 0 vs 1```...
