Question: Hi,

As I needed RNAseq raw sequencing data I downloaded the rnaseq manifest file from GDC legacy archive and with the token I downloaded rnaseq raw data.

The manifest looks like this:

id	filename	md5	size	state
d1017f74-3a39-4427-af57-273e34247b49	UNCID_2207021.7b9569bc-f513-4b64-9a7c-7bb53b9be79b.110801_UNC12-SN629_0115_BD0DVEABXX_3_ACAGTG.tar.gz	ed7f23aa9540ef0242cb6ddde30d1aca	5830465428	live
5e2d5c52-596f-49bc-967c-42129abbacbf	UNCID_2208720.71b58051-3bf8-4dfb-a431-c8aceab7c799.110608_UNC13-SN749_0073_BD0CV8ABXX_2.tar.gz	b1f03852b2ac3c3cd50cb4a87f2a116a	7587398372	live
2ef74f93-5da2-454c-aca2-d86c289eacb8	UNCID_2206802.25be50e7-7705-492d-a44a-0e40180d10c8.110901_UNC12-SN629_0127_BC025UABXX_1_CTTGTA.tar.gz	a965da78ada814a35702fd65209b500a	7867889236	live
e01ca3e0-beb0-46b7-bb7c-f5b16f966918	UNCID_2521679.d817dcee-1322-4949-a6e9-138447e6fc56.140417_UNC13-SN749_0343_BC41HBACXX_5_CTTGTA.tar.gz	6e6a26fcce8e84d209b1475249a922de	5187498148	live
992a7083-28ce-4857-898e-9d4b4fbf2fa1	UNCID_2319278.bf92b8cc-9a5c-4e96-917c-c264fe588f8d.131118_UNC12-SN629_0336_AC31D0ACXX_5_ACTTGA.tar.gz	bb9e19a5f286ff37bf95cb0c307930ea	6717741168	live
230082b7-39ec-4fe1-b3c6-daf35458f396	UNCID_2206889.526da11e-9125-4fcd-98d7-02994c9783d1.110810_UNC10-SN254_0263_AB09WEABXX_3_CAGATC.tar.gz	d93777efebc921e2539aa2b7081da6d4	4766879929	live
9bbada51-d827-4eea-af45-47d7b5ba137e	UNCID_2206522.147d6ebb-7359-449a-9e6a-6c8443ebaa2e.110919_UNC13-SN749_0113_AB00WUABXX_3_CGATGT.tar.gz	7bcfe71256ba172fa605bc4ddc04f9c7	7606309309	live
db1b68b0-dc0a-48a5-8acb-4cd45ea186e2	UNCID_2664315.22fe5cac-0623-4d0a-a158-f15fb5477d8f.120710_UNC12-SN629_0215_BC0WRNACXX_3_CTTGTA.tar.gz	281083ac338f67145ede3d8ef3f4300f	7504345358	live

After the download I have folders with names present in "id" column. Inside each folder there is tar.gz file.

For eg:

d1017f74-3a39-4427-af57-273e34247b49
|___ UNCID_2207021.7b9569bc-f513-4b64-9a7c-7bb53b9be79b.110801_UNC12-SN629_0115_BD0DVEABXX_3_ACAGTG.tar.gz

When I extracted the tar.gz files I got the fastq files like below:

110801_UNC12-SN629_0115_BD0DVEABXX.3_1.fastq
110801_UNC12-SN629_0115_BD0DVEABXX.3_2.fastq

What is the sample name here? Looks very confused.

Answer: Best way to do it.

library(GenomicDataCommons)
manifest <- read.table("gdc_manifest_rnaseq_fastq.txt")

manifest:

id filename md5 size state
d1017f74-3a39-4427-af57-273e34247b49 UNCID_2207021.7b9569bc-f513-4b64-9a7c-7bb53b9be79b.110801_UNC12-SN629_0115_BD0DVEABXX_3_ACAGTG.tar.gz ed7f23aa9540ef0242cb6ddde30d1aca 5830465428 live
5e2d5c52-596f-49bc-967c-42129abbacbf UNCID_2208720.71b58051-3bf8-4dfb-a431-c8aceab7c799.110608_UNC13-SN749_0073_BD0CV8ABXX_2.tar.gz b1f03852b2ac3c3cd50cb4a87f2a116a 7587398372 live
2ef74f93-5da2-454c-aca2-d86c289eacb8 UNCID_2206802.25be50e7-7705-492d-a44a-0e40180d10c8.110901_UNC12-SN629_0127_BC025UABXX_1_CTTGTA.tar.gz a965da78ada814a35702fd65209b500a 7867889236 live
e01ca3e0-beb0-46b7-bb7c-f5b16f966918 UNCID_2521679.d817dcee-1322-4949-a6e9-138447e6fc56.140417_UNC13-SN749_0343_BC41HBACXX_5_CTTGTA.tar.gz 6e6a26fcce8e84d209b1475249a922de 5187498148 live
992a7083-28ce-4857-898e-9d4b4fbf2fa1 UNCID_2319278.bf92b8cc-9a5c-4e96-917c-c264fe588f8d.131118_UNC12-SN629_0336_AC31D0ACXX_5_ACTTGA.tar.gz bb9e19a5f286ff37bf95cb0c307930ea 6717741168 live
230082b7-39ec-4fe1-b3c6-daf35458f396 UNCID_2206889.526da11e-9125-4fcd-98d7-02994c9783d1.110810_UNC10-SN254_0263_AB09WEABXX_3_CAGATC.tar.gz d93777efebc921e2539aa2b7081da6d4 4766879929 live
9bbada51-d827-4eea-af45-47d7b5ba137e UNCID_2206522.147d6ebb-7359-449a-9e6a-6c8443ebaa2e.110919_UNC13-SN749_0113_AB00WUABXX_3_CGATGT.tar.gz 7bcfe71256ba172fa605bc4ddc04f9c7 7606309309 live
db1b68b0-dc0a-48a5-8acb-4cd45ea186e2 UNCID_2664315.22fe5cac-0623-4d0a-a158-f15fb5477d8f.120710_UNC12-SN629_0215_BC0WRNACXX_3_CTTGTA.tar.gz 281083ac338f67145ede3d8ef3f4300f 7504345358 live

file_uuids <- manifest$id
head(file_uuids)

d1017f74-3a39-4427-af57-273e34247b49
5e2d5c52-596f-49bc-967c-42129abbacbf
2ef74f93-5da2-454c-aca2-d86c289eacb8
e01ca3e0-beb0-46b7-bb7c-f5b16f966918
992a7083-28ce-4857-898e-9d4b4fbf2fa1
230082b7-39ec-4fe1-b3c6-daf35458f396
9bbada51-d827-4eea-af45-47d7b5ba137e
db1b68b0-dc0a-48a5-8acb-4cd45ea186e2

library(GenomicDataCommons)
library(magrittr)

TCGAtranslateID = function(file_ids, legacy = TRUE) {
info = files(legacy = legacy) %>%
filter( ~ file_id %in% file_ids) %>%
select('cases.samples.submitter_id') %>%
results_all()
# The mess of code below is to extract TCGA barcodes
# id_list will contain a list (one item for each file_id)
# of TCGA barcodes of the form 'TCGA-XX-YYYY-ZZZ'
id_list = lapply(info$cases,function(a) {
a[[1]][[1]][[1]]})
# so we can later expand to a data.frame of the right size
barcodes_per_file = sapply(id_list,length)
# And build the data.frame
return(data.frame(file_id = rep(ids(info),barcodes_per_file),
submitter_id = unlist(id_list)))
}

res = TCGAtranslateID(file_uuids)
head(res)

file_id Submitter_id
d1017f74-3a39-4427-af57-273e34247b49	TCGA-E9-A1NA-11A
5e2d5c52-596f-49bc-967c-42129abbacbf	TCGA-AO-A12H-01A
2ef74f93-5da2-454c-aca2-d86c289eacb8	TCGA-AC-A23E-01A

I found the soution from seandavis blog https://seandavi.github.io/post/2017/12/genomicdatacommons-example-uuid-to-tcga-and-target-barcode-translation/