Individual whole genome sequence data download FASTQ

Question

[stefan.mester]

Hey there,

I am looking for a site to download whole genome sequence data from individuals to use in a study to compare with WGS sets of patients, that we sequenced in house.

We also sequenced one HapMap sample to use as a reference but more references are always good ;)

I looked at the sequence read archive of NCBI, the 1000 genome project etc. but seem to be to stupid to find suitable, preferably Illumins HiSeq 2000 FASTQ-files to do the mapping myself, data.

Does anyone have a good resource? I would appreciate it a lot

Thanks in advance and cheers

stefan

[PoGibas]

I didn't get it, are you looking for human reference genome?

[stefan.mester]

hey,

Sorry if I didn't explain to well, I will try again ;)

I am not looking for the human reference genome, that I have to do the mapping and use it to map FASTQ files to create the BAM-files.

I have raw sequence reads (FASTQ files) of patients sequenced myself and for further analysis I need raw sequence reads of more individuals that I can use to compare to the DNA of my patients.

I hope I made my problem clearer, if not keep on firing questions.

Cheers
Stefan

Answer 1

[Pierre Lindenbaum]

looked at the sequence read archive of NCBI, the 1000 genome project etc. but seem to be to stupid to find suitable, preferably Illumins HiSeq 2000 FASTQ-files to do the mapping myself, data.

search in the ftp indexes of the 1000 genomes project:

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/sequence.index" | grep  -E '(FASTQ_FILE|WGS)' | grep -E '(HiSeq 2000|FASTQ_FILE)' | grep -v '/ERR' | head -n 10 | verticalize

>>> 2
$1            FASTQ_FILE : data/HG02654/sequence_read/SRR588495.filt.fastq.gz
$2                   MD5 : dd5d09d06e1d9480d0344ed8bdc10007
$3                RUN_ID : SRR588495
$4              STUDY_ID : SRP004077
$5            STUDY_NAME : 1000 Genomes PJL WGS sequencing
$6           CENTER_NAME : BI
$7         SUBMISSION_ID : SRA059511
$8       SUBMISSION_DATE :
$9             SAMPLE_ID : SRS290936
$10          SAMPLE_NAME : HG02654
$11           POPULATION : PJL
$12        EXPERIMENT_ID : SRX194638
$13  INSTRUMENT_PLATFORM : ILLUMINA
$14     INSTRUMENT_MODEL : Illumina HiSeq 2000
$15         LIBRARY_NAME : Sage-109754
$16             RUN_NAME : C0W2YACXX120811.5.tagged_474.bam
$17       RUN_BLOCK_NAME :
$18          INSERT_SIZE : 402
$19       LIBRARY_LAYOUT : PAIRED
$20         PAIRED_FASTQ :
$21            WITHDRAWN : 0
$22       WITHDRAWN_DATE :
$23              COMMENT :
$24           READ_COUNT : 14621
$25           BASE_COUNT : 1476721
$26       ANALYSIS_GROUP : low coverage
<<< 2

>>> 3
$1            FASTQ_FILE : data/HG02654/sequence_read/SRR588495_1.filt.fastq.gz
$2                   MD5 : 12d15fb64f40c930ad567e06d60784a5
$3                RUN_ID : SRR588495
$4              STUDY_ID : SRP004077
$5            STUDY_NAME : 1000 Genomes PJL WGS sequencing
$6           CENTER_NAME : BI
$7         SUBMISSION_ID : SRA059511
$8       SUBMISSION_DATE :
$9             SAMPLE_ID : SRS290936
$10          SAMPLE_NAME : HG02654
$11           POPULATION : PJL
$12        EXPERIMENT_ID : SRX194638
$13  INSTRUMENT_PLATFORM : ILLUMINA
$14     INSTRUMENT_MODEL : Illumina HiSeq 2000
$15         LIBRARY_NAME : Sage-109754
$16             RUN_NAME : C0W2YACXX120811.5.tagged_474.bam
$17       RUN_BLOCK_NAME :
$18          INSERT_SIZE : 402
$19       LIBRARY_LAYOUT : PAIRED
$20         PAIRED_FASTQ : data/HG02654/sequence_read/SRR588495_2.filt.fastq.gz
$21            WITHDRAWN : 0
$22       WITHDRAWN_DATE :
$23              COMMENT :
$24           READ_COUNT : 2415523
$25           BASE_COUNT : 243967823
$26       ANALYSIS_GROUP : low coverage
<<< 3

>>> 4
$1            FASTQ_FILE : data/HG02654/sequence_read/SRR588495_2.filt.fastq.gz
$2                   MD5 : da0f8bec3077c6e84ea700f742390dae
$3                RUN_ID : SRR588495
$4              STUDY_ID : SRP004077
$5            STUDY_NAME : 1000 Genomes PJL WGS sequencing
$6           CENTER_NAME : BI
$7         SUBMISSION_ID : SRA059511
$8       SUBMISSION_DATE :
$9             SAMPLE_ID : SRS290936
$10          SAMPLE_NAME : HG02654
$11           POPULATION : PJL
$12        EXPERIMENT_ID : SRX194638
$13  INSTRUMENT_PLATFORM : ILLUMINA
$14     INSTRUMENT_MODEL : Illumina HiSeq 2000
$15         LIBRARY_NAME : Sage-109754
$16             RUN_NAME : C0W2YACXX120811.5.tagged_474.bam
$17       RUN_BLOCK_NAME :
$18          INSERT_SIZE : 402
$19       LIBRARY_LAYOUT : PAIRED
$20         PAIRED_FASTQ : data/HG02654/sequence_read/SRR588495_1.filt.fastq.gz
$21            WITHDRAWN : 0
$22       WITHDRAWN_DATE :
$23              COMMENT :
$24           READ_COUNT : 2415523
$25           BASE_COUNT : 243967823
$26       ANALYSIS_GROUP : low coverage
<<< 4

>>> 5
$1            FASTQ_FILE : data/HG02696/sequence_read/SRR588497.filt.fastq.gz
$2                   MD5 : 04182f5744883fac63c0f7bfe3b56fe2
$3                RUN_ID : SRR588497
$4              STUDY_ID : SRP004077
$5            STUDY_NAME : 1000 Genomes PJL WGS sequencing
$6           CENTER_NAME : BI
$7         SUBMISSION_ID : SRA059511
$8       SUBMISSION_DATE :
$9             SAMPLE_ID : SRS290951
$10          SAMPLE_NAME : HG02696
$11           POPULATION : PJL
$12        EXPERIMENT_ID : SRX194639
$13  INSTRUMENT_PLATFORM : ILLUMINA
$14     INSTRUMENT_MODEL : Illumina HiSeq 2000
$15         LIBRARY_NAME : Sage-109762
$16             RUN_NAME : D1314ACXX120814.6.tagged_581.bam
$17       RUN_BLOCK_NAME :
$18          INSERT_SIZE : 391
$19       LIBRARY_LAYOUT : PAIRED
$20         PAIRED_FASTQ :
$21            WITHDRAWN : 0
$22       WITHDRAWN_DATE :
$23              COMMENT :
$24           READ_COUNT : 13615
$25           BASE_COUNT : 1375115
$26       ANALYSIS_GROUP : low coverage
<<< 5

[scchess]

File not found... Can you please check?

[Pierre Lindenbaum]

this thread is 2.6 years old. Can YOU please search for it.