Question: (Closed) Length of reads in a RNAseq experiment
0
gravatar for Carlos Andrés Caicedo
2.2 years ago by
Colombia/Medellín

Should all the reads of my experiment be of the same length if I am going to perform a de novo assembly?

The raw data contained reads of the same length but after the trimming process by quality some of them are reduced. I would like to know if there are some effect in the downstream analysis with this reads. (The majority of the reads remain of the same length and only a few reads have been trimmed)

Thanks

Carlos Andrés.

ADD COMMENTlink written 2.2 years ago by Carlos Andrés Caicedo0

Which tools do you plan to use?

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k

I am going to use Rockhopper.

ADD REPLYlink written 2.2 years ago by Carlos Andrés Caicedo0

I am not familiar with that tool and I did not find it wrapped for Galaxy. It is probably best to ask this question of the tool developers (http://cs.wellesley.edu/~btjaden/Rockhopper/) or on a more general bioinformatics forum (https://www.biostars.org) for the best feedback/advice from those that use it.

I am going to close this question out as non-Galaxy related post.

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k

Hello dear Jennifer Hillman-Jackson

I have already made the question in Biostar

I thank you for your help and I apologize for the mistake.

Cheers!

ADD REPLYlink written 2.2 years ago by Carlos Andrés Caicedo0

Hello candres.caicedo!

We believe that this post does not fit the main topic of this site.

Not about Galaxy

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k
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