songeric1107

I am trying to combine WT and mutant object together and get the DE peaks by comparing wt and mutant. do you have a good example for that? I am...

vcf2maf could not specify the output path

1

trying to run the script as follows by specifying the output path, however, get an error as follows. perl /usr/local/packages/vcf2maf/vcf2maf.pl --input-vcf /local/devel/ysong/vcf2maf/mskcc-vcf2maf-754d68a/tests/test.vcf --output-maf /local/scratch/ysong/test.vep.maf --vep-path /usr/local/packages/miniconda3/envs/vep/bin MSG: ERROR: Output file...

plotAvgProf2 failed

1

>ChIPseeker::plotAvgProf2(peak1,TxDb = txdb, conf = 0.95, by = "gene", type = "body",weightCol = "V5",ignore_strand = F) >> preparing promoter regions... 2021-12-08 03:25:48 PM >> preparing tag matrix... 2021-12-08 03:25:48 PM...

how to run vcf2maf with clinvar db

2

I have vcf files which are generated using freebay, how could I add the clinvar annotation to the vcf and convert to maf? I try to run as following vep...

try to run as following msisensor-pro scan -d /local/db-build/gatk/hg38/Homo_sapiens_assembly38.fasta -o /local/scrath/test/homo.list always get errors as following failed to open file: /local/scrath/test/homo.list

all unassigned for 10x single cell RNAseq dataset using 1000genome vcf

3

Hi Huang, Thanks for reading my previous issue. I had another problem. I am trying to apply vireo with scRNAseq datasets based on 1000 genome vcf file. However, all the...