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).
When initally running gemBS extract, I do not see any variants in the _snps.txt.gz files. The he _snps.txt.gz file is empty. I execute the following commands to extract wgbs samples...
What is the difference between these two binaries? ``` /home/dlin/.conda/envs/gembs/bin/bs_call /home/dlin/.conda/envs/gembs/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call ``` I've noted that the first one does not have options such as `-O` and `--contig-sizes`. The .vcf generated...
With this command, I'm encountering an error: ```shell /usr/local/anaconda/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call -r /ref/hg38_no_alt.gemBS.ref \ -n TGACCA \ --contig-bed /out_dir///calls/TGACCA/contigs_TGACCA_chr4.bed \ --contig-sizes /ref/hg38_no_alt.contig.sizes \ --report-file /out_dir///calls/TGACCA/TGACCA_chr4.json \ --right-trim 0 \ --left-trim 0 \...
When I tried to read the documentation, I found that the 404 page not found error happened, it has lasted for about 2 weeks. But I could read that two...
When doing methylation (indexing, mapping, calling, extraction) and SNP (indexing, mapping, calling, extraction), for the four steps (indexing, mapping, calling, extraction), which steps should be different when doing methylation or...