Starting with whole genome sequencing data

Question

[zizigolu]

Hi,

I have been assigned whole genome sequencing data of tumour samples of responder and non-responder patients to a drug exactly with this data file;

case_rna_ids.txt
pheno.copynumber.caveman.csv.tar
pheno.passed.somatic.indel.vcf.tar
pheno.snv.pass.vcf.tar
pheno.SVannotated.txt.tar
pheno_case_dna_rna_ids.txt
pheno_case_rna_ids.txt
pheno_dna_mut_sigs.txt
pheno_rna_rpkm.txt.tar
rna_rpkm.txt copy.tar
rna_rpkm.txt.tar
trg.passed.somatic.indels.vcf.tar
trg.snp.pass.vcf.tar
trg_case_dna_ids.txt

I am googling, I guess I should annotate these mutations to see which one affects the gene expression. I uploaded one of pheno.passed.somatic.indel.vcf in Ensembl Variant Effect Predictor (VEP) and job is running likely finishing one ticket takes long time though.

Anyone please have experience with such files to tell me how could I start?

[WouterDeCoster]

Temporarily reduced functionality of Ensembl and Ensembl Genomes

[Benn]

Don't you think you should read something about this subject first before you start working with it? That's how I usually approach new methods and applications.

[zizigolu]

Thank you, I just started this morning. I am just wondering why I have 25 patients while I have 154 pheno.RNA.passed.somatic.indel.vcf files

I uploaded some of my files in Ensembl Variant Effect Predictor (VEP) , results is a big file I am trying to learn what that is but first I should know what these files are

[Benn]

Why don't you ask the one that gave these files to you?

[zizigolu]

Files come from Cambridge, this guy says he just knows we have 25 patients

[Benn]

If this guy doesn't know what he has done, how do you expect we know it??

[zizigolu]

Sorry, I meant maybe somebody knows it is possible one patient could have different files for each variant

[Benn]

I think your post does not have enough information, you should explain which methods and tools were used to get your results. Files come from Cambridge from a guy is not helpful. Or is Cambridge a tool?

[zizigolu]

Sorry, you right. I am waiting for technician to get more information about files then perhaps I would start my questions about analysis