How to submit your data.
Data can be uploaded either through the
ISMARA website
, or by using the
ISMARA uploader python script.
There are three possible ways to submit the data to ISMARA:
-
Upload files from your own computer.
-
Provide a list of URL links to the data files.
-
Provide a list of SRR IDs.
Uploading files on the website
-
First provide your email address and a name for
your project. ISMARA will notify you via email
when its analysis of your data is ready, and use
the project name for reference.
-
Select your data type, i.e. whether you have micro-array, RNA-seq,
or ChIP-seq data.
-
Select the appropriate organism/genome assembly.
-
Inclusion of miRNA regulation in the analysis can
be turned off if desired.
-
Click the "add files" button and select all the
files you want to upload. Note you can click the
button multiple times.
-
Click the "Start upload" button.
File formats
-
For micro-array data ISMARA expects CEL files. A
list of supported Affymetrix chips is available
here.
-
RNA-seq and ChIP-seq data can be provided as
FASTQ, BED, BAM, or SAM files. Note that when
using data that is already mapped it is essential
that the genome assembly matches the one you
selected above.
-
There should be one file per biological sample,
except for paired-end FASTQ files. For paired-end
FAST files, pairs of files with the name
convention sampleX_R1.fastq and sampleX_R2.fastq
should be used.
-
Choose informative files names because ISMARA will use the file names to
refer to the samples in its results.
-
You are encouraged to compress your files with
gzip or zip. Tar or zip archives with multiple
files are allowed. Please do NOT use
subdirectories in your archive.
List of URLS.
-
First make sure you provided a contact email and
selected the correct data type and
organism/genome assembly.
-
Paste URLs with the links to the data files (an
example with two ftp URLs is provided).
-
There should be one line/URL per biological sample.
-
Click the "Submit links" button.
List of SRR IDs.
