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Question: Occurence of reads
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gravatar for viktoria.preiser
4.6 years ago by
viktoria.preiser • 0
Austria
viktoria.preiser • 0 wrote:

Hi,

I already obtained the sequences with the right length. But now I would like to know how often on read occurs.

For example like that kind of output: AATGCCGGACCTTTTA 34560

So that I have a list with the sequence and next to the sequence the number of occurance. Is something like that possible with the Galaxy Software? By the way: I'm using the online platform.

Thanks so much and all the best,

Viktoria
number of reads galaxy • 771 views
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modified 4.6 years ago • written 4.6 years ago by viktoria.preiser • 0
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gravatar for Bjoern Gruening
4.6 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Viktoria,

I assume you have your file in fasta format. If so than you can convert your fasta file into a tabular file with ``STA-to-Tabular converter``. In a next step you can group your data with ``Group data by a column and perform aggregate operation on other columns.`` and count on your sequence column. You will get back a file with all sequences and all counts.

If you do not have a fasta file, the tool ``FASTQ to FASTA converter`` will help you.

Cheers,

Bjoern
ADD COMMENT • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k
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gravatar for viktoria.preiser
4.6 years ago by
viktoria.preiser • 0
Austria
viktoria.preiser • 0 wrote:

Hi Bjoern,

that helped me so much :). Thank you!!

Cheers, Viktoria
ADD COMMENT • link written 4.6 years ago by viktoria.preiser • 0
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