gemBS
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heathsc
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
How do I activate define the GPU for read mapping? I did go though the working example and used nvidia-smi to monitor any potential activity on the GPU: I could...
When initally running `gemBS extract`, I do not see any variants in the `_snps.txt.gz` files. The gemBS config refers to the following Reference and DBSNP: ``` ... reference = ${root}/ref/human_g1k_v37.fasta.gz...
Why do the statistics of high and low methylation sites in the _cpg.bed file not agree with the results of REPORT? I see that the report is the result of...
If I have the following samplesheet: ``` Barcode,File_id,end_1,end_2 S001,S001,sample1_R1.fq.gz,sample1_R2.fq.gz S001,S001_1,sample1_1_R1.fq.gz,sample1_1_R2.fq.gz ``` (i.e. in cases with multiple rows for single barcode, one of the file_id is equal to the barcode): Then...
Hi, I used the config files on UserGuide(includes IHEC_standard.conf and IHEC_PBAT.conf) to run the gemBS on a PBAT datasets. But it failed in the calling step, and I can't tell...
Hello, We are seeing an odd error trying to map one particular fastq. I checked the resource utilization and didn't see anything excessive. I'm quite confident it's not a fastq...
Hello, I was interested in testing out gemBS, but I'm a bit confused about how the indices are built. From the documentation, I can't figure out if there is a...
Hello, We are using Cromwell on a Google Cloud Platform to analyze sequencing data. We found that, at least for bwa and WGS, scattering the reads in small chunks across...
Hello, We are using `gemBS` version 3.5.1 and the [IHEC standard configuration](https://github.com/heathsc/gemBS/blob/master/gemBS/etc/gemBS_configs/IHEC_standard.conf). When loading the ENCODE-style CpG bigBed produced during `gemBS extract` into the UCSC browser as a custom track,...
Dear all, I am learning how to better use gemBS to analysis the whole-genome bisulfite sequencing data. During testing using the example data, I found that it is difficult for...
