Question: Small RNA Seq Analysis for newcomers...
0
gravatar for tushar131189
4 months ago by
tushar1311890 wrote:

Hello all...I am using this platform very first time.

I am working on two rice cultivars with contrasting salt tolerance nature. I have received the raw data of small RNA sequencing and now trying to perform the downstream analysis of the same.

Frankly I dont have much experience in such kind of in silico analysis, Plus we are not provided with any paid softwares to do so.

So can anyone please suggest me the simplest pipeline for miRNA analysis. Any kind of help is deeply appreciated.

Thanks

rna-seq • 180 views
ADD COMMENTlink modified 5 weeks ago • written 4 months ago by tushar1311890
1

Do you have any unix command line expertise? If you don't, then Galaxy may be your only free option, that may or may not work.

smallRNA seq data may require custom trimming based on the kit used. Do you know what kind of kit was used to prep your data and what type of sequencing this is.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax85k

Thanks genomax....Yes I will have those details.. Actually I have received the analyzed data, but i want to re-do all the analysis by myself.

ADD REPLYlink written 4 months ago by tushar1311890

Hi Tushar,

Could you please let me know which pipeline you found to small RNA seq analysis? I am starting to analyze small RNA seq and your suggestion will help me a lot and I appreciate you a lot.

Thanks

ADD REPLYlink written 10 weeks ago by m.s_tabatabaei0

Hi m.s_tabatabaei

We have received a data analysed using the UEA Small RNA Workbench version 2.4. However, I am still not able to learn each and every step of the analysis. What pipeline you are using? I would like to learn and understand the same thing. I am just not able to run the whole analysis as minor detail-steps for any analysis are not provided anywhere. Any kind of help in this regard will be helpful. Appreciate your time.

Thanks.

ADD REPLYlink written 5 weeks ago by tushar1311890
1

Looks like there are tutorials available for the Workbench you mention. Since the workbench seems to be available for many OS you should be able to repeat the analysis yourself.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax85k

Hi Tushar,

I am searching to find a good pipeline for plant small RNA seq. I worked with annotation and merge pipeline on CLC but I don't know which data in output should be considered as input to analyze differential expression. I worked with miRDeep2 as well but I am not sure it is good for plants or not. I think miRDeep-P2 is better. Please let me know if you found any good pipeline for small RNA seq analysis on plants. Thanks, Mina

ADD REPLYlink written 18 days ago by m.s_tabatabaei0
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