lizhan96

question about calling CNV with tumor and normal-pair sample

3

Dear developer I want to call CNV with my tumor sample(array data), and the normal-pair sample i had. When I run the MoChA pipeline, some hg19/hg39 related files was needed....

question with call cnv for array data

8

hi there, I have successfully run the phase pipeline. but it's seem that the Chromosomal alterations pipeline guileline was only described for the WGS data but not array data? Could...

how to convert CEL to CHP?

2

After I install bcftools, I follow the README document and run the following code, but there is a error message. `path_to_output_folder="..." cel_list_file="..." apt-probeset-genotype \ --analysis-files-path . \ --xml-file GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml \...

ERROR in converting CHP to VCF

1

hi, devoloper. After I install bcftools-1.11 and gtc2vcf, I run the following code `/data_6t/lizhan/02.software/bcftools-1.11/bcftools +affy2vcf \ --no-version -Ou \ --csv $csv_manifest_file \ --fasta-ref $ref \ --chps $path_to_chp_folder \ --snp $path_to_txt_folder/AxiomGT1.snp-posteriors.txt...

对小鼠进行kegg注释，无法得到注释结果。

5

``` > kegg_enrich No gene can be mapped.... --> Expected input gene ID: --> return NULL... ``` 我分别尝试使用symbol，entrezid作为输入都没有得到结果，此处“Expected input gene ID: ”也没有提示相应输入格式，是否是相关库下载出问题的原因？