menghaowei / detect-seq Goto Github PK
View Code? Open in Web Editor NEWAn unbiased method for genome-wide CBE off-targets assessment
License: Other
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Bismark vs HiSAT2?
The Nature Methods paper (https://www.nature.com/articles/s41592-021-01172-w) describes the read alignment step using Bismark, but the workflow and code shown here uses HiSAT2. Was there any reason for the switch?
Missing snv info files
The following command failed. Could you provide these files: snv_info/293T-snv_info.list1.bed and snv_info/293T-snv_info.list2.vcf ? Thanks!
python pmat-merge.py -i ${out_C_pmat} -f C -t T -r ${ref_genome_fa} -d 50 -D 100 --NoMutNumCutoff 2 --OmitTandemNumCutoff 2 -o ${out_CT_mpmat} --SNP snv_info/293T-snv_info.list1.bed,snv_info/293T-snv_info.list2.vcf 2> ${out_CT_log} &
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