Question: COSMIC copy number variant data
0
gravatar for rajesh
13 months ago by
rajesh 60
India/Chandigarh/
rajesh 60 wrote:

Hello everyone, I am working on COSMIC copy number variant data, i have dowloaded the .csv file for pancreatic cancer. In this file SAMPLE_NAME column contain the info for source of the sample. For my work i required CNV of tissue sample only. Here in this column some cell line names and some IDs are there. Is the ID corresponds to TCGA/ICGC data. Because in file description it is written that COSMIC contain data from ICGC and TCGA. Can anyone tell me that how to extract from this file only CNV of tissue origin rather than cell line. Thanks in advance

CNV_ID   ID_GENE     GENE_NAME   ID_SAMPLE   ID_TUMOUR   PRIMARY_SITE    SITE_SUBTYPE_1  SITE_SUBTYPE_2  SITE_SUBTYPE_3  PRIMARY_HISTOLOGY   HISTOLOGY_SUBTYPE_1     HISTOLOGY_SUBTYPE_2     HISTOLOGY_SUBTYPE_3     SAMPLE_NAME     TOTAL_CN    MINOR_ALLELE    MUT_TYPE    ID_STUDY    GRCH    CHROMOSOME_G_START_G_STOP  
6202170 3407    KDM5D   724869  616273  pancreas    NS  NS  NS  carcinoma   ductal_carcinoma    NS  NS  HPAF-II 0   0   loss    619 37  Y:21409706..23649449  
6202156 91964   ENSG00000183704 724869  616273  pancreas    NS  NS  NS  carcinoma   ductal_carcinoma    NS  NS  HPAF-II 0   0   loss    619 37  Y:10012012..14423723  
126953  101951  NUP43_ENST00000367403   1653055 1567842 pancreas    NS  NS  NS  carcinoma   ductal_carcinoma    NS  NS  8012424 3   null    gain    328 37  6:149780474..151830769  
126953  107946  IYD_ENST00000392255 1653055 1567842 pancreas    NS  NS  NS  carcinoma   ductal_carcinoma    NS  NS  8012424 3   null    gain    328 37  6:149780474..151830769
rna-seq snp • 453 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by rajesh 60

What have you tried? Have you looked at COSMIC documentation to figure out fields potentially differentiating tissue sample vs cell line somatic mutation entries?

ADD REPLYlink modified 13 months ago • written 13 months ago by RamRS21k

Thanks for you response, I have the complete annotation file for COSMIC CNV. I couldnt figure out what are IDs in SAMPLE_NAME signifies.

ADD REPLYlink written 13 months ago by rajesh 60

EDIT: It seems like your answer was deleted without actually moving the information to the right spot, so I've restored your answer as a comment. Please be more careful in the future.


Hello rajesh ,

This reply is better suited as a reply to my comment. Could you make the appropriate change please? That would involve the following steps:

  1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + clink link to open it in a new tab) and do a Select All -> Copy there.
  2. Click on "Add Reply" on my comment here: C: COSMIC copy number variant data
  3. Paste the copied text
  4. Click on the green "Add Comment" button
  5. Click on moderate back in your answer here: A: COSMIC copy number variant data
  6. Choose Delete Post
  7. Click on the blue Submit button.

Thank you!

ADD REPLYlink modified 13 months ago • written 13 months ago by RamRS21k
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