This Windows GUI tool created in Windows Forms generates a query from a list of TCGA ids to be used at portal.gdc.cancer.gov/query. It can also directly download the manifest file instead.
Select a file containing a list of TCGA ids. Ids can be quoted or unquoted. Only the first 12 characters of each ID is used.
Input file:
TCGA-05-4250
"TCGA-05-4405"
TCGA-05-4415-0192
"TCGA-05-4417-0164"
The type of files to query. Either mRNA (.htseq.counts, .FPKM.txt, and .FPKM-UQ.txt) miRNA (.isoforms.quantification.txt) or both.
The query will be copied to the user's clipboard, which can be pasted at portal.gdc.cancer.gov/query. Keep in mind longer queries are slow on the website; using the Download Manifest feature is ideal.
Query type: mRNA
Clipboard output:
files.file_name in ["*.htseq.counts*", "*.FPKM.txt*", "*.FPKM-UQ.txt*"] and cases.project.program.name in ["TCGA"] and cases.submitter_id in ["TCGA-05-4250","TCGA-05-4405","","TCGA-05-4415","","TCGA-05-4417"]
This action downloads a manifest file containing all of the files found by the query and a metadata file containing information about those cases. Requires an internet connection to function. Note: if the file name the user selects to save the manifest to already exists, a new file will be created with a version number appended.
Query type: mRNA
Manifest output:
id filename md5 size state
10b6df33-8f32-4ed9-b1b1-8867be485a2f 6e98ba8f-e00d-470c-832f-adc3dc6956a6.FPKM.txt.gz 61e93edfed714da7280bba70c08d0f41 505452 released
a07c86e4-b157-49f7-b541-7e1c0b3cf27b 4ed68c20-e7f2-4b40-97f1-4f8a3ddae0a9.FPKM.txt.gz 895c980876df6ecde9fdb681edec209e 514950 released
46ea8adf-e1bd-4e3b-8cea-307ca36073d0 6e98ba8f-e00d-470c-832f-adc3dc6956a6.FPKM-UQ.txt.gz 7ca897843589d989fcd429af53b3cad0 505835 released
3653dfea-049c-4ae8-8aca-cf6799797dd7 dc76cdde-f77f-4604-94c4-0b150b9a56b4.htseq.counts.gz 71bcd107585e69b96e909076cc9c1b61 249745 released
156acd96-fb20-4083-ace0-db465133670c d011c9fc-3598-4f0b-b059-85d63de31a9f.FPKM.txt.gz 5970f4595f6d210bfd1f9b65b045a972 501941 released
0f5f287b-ee07-47b1-9d71-03cacffbdc21 dc76cdde-f77f-4604-94c4-0b150b9a56b4.FPKM-UQ.txt.gz 03d16f7df1a9a79f7b764bb2e5ee0005 512590 released
545b3be7-9189-4e1e-85d6-af4a7540ec97 4ed68c20-e7f2-4b40-97f1-4f8a3ddae0a9.htseq.counts.gz 2098e89ef4ad8b42d27bd05b38d933b4 253840 released
3471e070-167d-4af2-b9c6-38fbd4e86add 4ed68c20-e7f2-4b40-97f1-4f8a3ddae0a9.FPKM-UQ.txt.gz cac01aaa0b0c89bfcb765b9cf606f26c 516514 released
9c740043-d02a-412a-851b-cfcb625e04c4 6e98ba8f-e00d-470c-832f-adc3dc6956a6.htseq.counts.gz 74b0373a0ccc28097775e4557fedfb00 249824 released
1fae764e-3807-4565-a78d-5ea852d327a7 d011c9fc-3598-4f0b-b059-85d63de31a9f.htseq.counts.gz 7207f6f35a1b2044035b700eb4e68aa9 248552 released
999f701a-2bd2-4e9d-94af-08d0f1be769c dc76cdde-f77f-4604-94c4-0b150b9a56b4.FPKM.txt.gz 80e7f3092027e21e879633c74596aa37 509899 released
96332d27-a064-4ca5-bf5d-f9c357556c39 d011c9fc-3598-4f0b-b059-85d63de31a9f.FPKM-UQ.txt.gz 9aadc0fd9352dccf65e509ecf186c8a7 503624 released