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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).

• 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.pl 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).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Publicly Archiving Data
 

Preferences end here -->

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

SRA main page

SRA login page

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.

• 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).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Publicly Archiving Data
 

Preferences end here -->

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.

Submitting Genome Sequencing Reads to the SRA

SRA main page

SRA login page

NCBI online SRA manual

Notes:

• You cannot change aliases in the normal upload area, so be careful to enter them correctly the first time!

• Illumina uploads must be in Illumina 1.5+ FASTQ format, not converted to Sanger FASTQ format.

Dryad

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

SRA main page

SRA login page

NCBI online SRA manual

Notes:

• You cannot change aliases in the normal upload area, so be careful to enter them correctly the first time!
• Be sure to use the MD5 checksum for the compressed file.
• Illumina uploads must be in Illumina 1.5+ FASTQ format, not converted to Sanger FASTQ format.

Submitting Genome Sequencing data to the SRA

Submitting Genome Sequencing data to the SRA

The NCBI online manual for the SRA.

Notes:

Be sure to use the MD5 checksum for the compressed file.