Re: [galaxy-user] Identifying Tags - Galaxy Question

Hi Dominique,

Glad that helped. And yes, you can merge many file types that are text-based with the tool 'Text Manipulation -> Concatenate datasets". Sometimes you will need to convert to format tabular first, and then back to the desired format (fasta, gtf, etc.) after.

Take care,

Jen Galaxy team

On 9/19/13 5:51 AM, D. A. Cowart wrote:

Thank you Jennifer, this helped tremendously. I completely missed the barcode splitter too. One other question: do you know if it is possible to merge different fasta files on Galaxy? Say, I wanted to merge those tagged files back to one complete fasta file.

Best, Dominique Cowart

On Thu, Sep 19, 2013 at 12:19 AM, Jennifer Jackson <jen@bx.psu.edu mailto:jen@bx.psu.edu> wrote:

Hello Dominique,

Yes, this can be done. Here is the process ->

Start by splitting up the data by using the 'NGS: QC and
manipulation -> Barcode Splitter" tool. The result files will be
available as links. These can be copied and added to the "Get Data
-> Upload File" tool in the text box, in batch, and each will
loaded as a dataset. Copying them into a simple text file, then
pasting into the Upload tool all at once is a quick way to do
this, or you can do one by one.

Once you have the individual files as datasets, you probably will
want to rename them to better keep track of which barcode/tag they
represent. Click on the pencil icon in the upper right corner of
each dataset to do this on the Edit Attributes form.

Next, the idea is to convert the fasta dataset to tabular, add in
a column with the "_Tag1" information, merge the original
identifier column with the new tag column, cut the columns to
rearrange - (you want just the new merged identifier and the
original fasta sequence - leaving behind the two columns with the
original identifier + tag), then covert back from tabular to fasta
format. Use the tools in 'Text Manipulation' and 'FASTA
manipulation' to do these operations. I would normally suggest
creating/using a workflow at this point, but as the tags will all
be different, and the "Add column" step is in the middle of the
processing, this is probably not worth it.

Hopefully this helps!

Jen
Galaxy team


On 9/18/13 7:36 AM, D. A. Cowart wrote:

...

Hello,

I need to perform an action (or series of actions) on an 454
dataset using Galaxy, and have not been able to figure out the
necessary steps, even after looking through the toolbar
expressions and using custom search.
My file is a fasta and has the standard format:

>GNJQDEZ01A940A
CTGAGTCAGGTCAACAATCATAAGATATTGGCACCATGTACCTGTGGTTCTCGTTTCC
ATGTTA
>GNJQDEZ01BJYQZ
CTGAGTCAGGTCAACAATCATAAGACATCGGCTCTCTATATTTAATATTGGT

Each of the 100,000 sequences within this file contains a
specific tag, which is the first 8 nucleotides.
There are 19 tags total. I would like to identify these tags and
add an identifier of the tag to the sequence name.
Therefore, if I am looking for the first tag (CTGAGTCA), the
output would look like:

>GNJQDEZ01A940A_*Tag1*
*CTGAGTCA*GGTCAACAATCATAAGATATTGGCACCATGTACCTGTGGTTCTCGTTTCC
ATGTTA

Is it possible to achieve this using Galaxy? If possible, could
you kindly suggest tools to use.

Thank you in advance,
Dominique Cowart


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