multiple_join_paired_ends.py

[Narasimhulu.N]

I had run multiple_joined_paired_ends.py for my files and there was no error in running the command. I got joined and unjoined (R1 & R2) files but the data of unjoined files is more (in Mbs) and the jopined file data is less (in Kbs). is there any possibilty of joined data involved in unjoined files. Can I proceed further with this type of data? 

I have used the following command:

multiple_join_paired_ends.py -i input_files -o output folder

Please help me.

Thank you.

With Regards

N.Narasimhulu

[Yoshiki Vázquez Baeza]

Hello,

Without knowing any of the specific details about your sequencing run, this makes sense. When you join sequences you are increasing the amount of data in the joined sequences, so it makes sense that the files increase in size right.

Thanks!

Yoshiki.

[Narasimhulu.N]

Thank you Yoshiki for early reply. This data is generated by using Miseq and 250*2. Data quality is good. When I have used the "SeqPrep" method, joined data is better. Please, explain what is difference between these two and which method is useful?.

Thank you.

[Yoshiki Vázquez Baeza]

Hello,

Would you mind elaborating on what you mean by "joined data is better"?

They are both different programs and as such they have different algorithms, I don't know about the specifics of each implementation. I suspect that the differences you are seeing may be a consequence of the default parameters that each program sets in its options.

https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqJoin.md

https://github.com/jstjohn/SeqPrep

Thanks!

Yoshiki.

[Narasimhulu.N]

Thank you Yoshiki for sharing links. After joining the paired-end data using SeqPrep method, joined data is with more reads.

Thank you once again for sharing your inputs.

[Narasimhulu.N]

Dear Mr. Yoshiki Vazquez Baeza,

I practiced tutorial data (moving_pictures_tutorial-1.9.0), every command were running fine. But I have small doubt for eigenvalues. I checked log file (cdout step) of tutorial results and my log file, The eigenvalues are different. I am using the same tutorial data, but why different eigenvalues are represented. I am using qiime 1.9.1 and I have qiime base installation only. Qiime full installation it showing 15=failures and 1=error.

Please clarify my small doubt.

Thank you.

[Antonio González Peña]

Eigenvalues and eigenvectors will change (hopefully slightly) based on your software stack and hardware so I wouldn't read much into it as long as the same clustering pattern is present. Hope this helps.

[Narasimhulu.N]

Thank you sir for your reply and explanation.