Publicly Archiving Data

These locations can give you accession numbers for data that may not be easily communicated as supplementary information for a research report. An advantage of submitting to these public databases is that your data will be archived in standard formats that others can use more easily.

Submitting Sequences to GenBank

The easiest way for a few sequences is to use the BankIt web submission tool.

The Geneious submission tool does not properly format GenBank submissions as of v6.06 (@JEB).

Submitting Genome Sequencing Reads to the SRA

external SRA main page
external SRA login page
external NCBI online SRA manual

Notes:

  • You cannot change aliases in the normal upload area, so be careful to enter them correctly the first time!
  • It is easiest to upload uncompressed FASTQ files.
  • Illumina uploads must be in Illumina 1.5+ FASTQ format, not converted to Sanger FASTQ format.
  • The flow cell number and lane are encoded in the name of every read in the FASTQ.
  • Paired-end or mate-paired FASTQ files must be interleaved (one file alternating corresponding first and second reads), rather than with all of the first reads in one file and all of the second reads in another file. The script interleave_paired_fastq.sh can construct the interleaved file.
  • The script estimate_insert_length.sh can be used to estimate the fragment size in a paired library to complete those fields.
  • Use the md5sum command to calculate the MD5 checksum for FASTQ files.

Dryad

Dryad is especially good for submitting large data tables and analysis scripts (e.g., in R).

Topic attachments
I Attachment Action Size Date Who Comment
shsh estimate_insert_length.sh manage 0.4 K 17 Feb 2013 - 17:25 Main.JeffreyBarrick  
shsh interleave_paired_fastq.sh manage 0.6 K 17 Feb 2013 - 17:26 Main.JeffreyBarrick  
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Topic revision: r4 - 17 Feb 2013 - 17:27:02 - Main.JeffreyBarrick
Lab.PubliclyArchivingData moved from Lab.ProtocolsUploadingDataToSRA on 14 Feb 2013 - 14:28 by Main.JeffreyBarrick - put it back
 
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