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Triplet Periodicity
28-Jul-2015, 06:55 AM
Post: #1
Triplet Periodicity
Hi,
I run the Triplet Periodicity script but for two times I got the same plot showing for each read length 0 values (pdf attached).
Any suggestions?Huh

Thanks a lot
Iole


Attached File(s)
.pdf  Periodicity-plot.pdf (Size: 4.4 KB / Downloads: 10)
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28-Jul-2015, 04:11 PM (This post was last modified: 28-Jul-2015 07:35 PM by vimalkumarvelayudhan.)
Post: #2
RE: Triplet Periodicity
Hi Iole,
You seem to have provided the right inputs for the triplet periodicity program. It is not clear why the plots are not being produced. We will contact the developers of the riboSeqR package about this issue and let you know when we get a response.

In the meantime, could you try using different Ribo/RNASeq data sets if you have them?

Regards,
Vimal
The RiboGalaxy Team
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31-Jul-2015, 10:28 AM
Post: #3
RE: Triplet Periodicity
Hi Iole,
An extra space at the end of the sequence headers in the FASTA file you had uploaded was causing the problem.

>BL00076_1 <- extra space here

Could you please reformat the file to remove the space and try repeating the triplet periodicity step again?

Regards,
Vimal
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21-Oct-2015, 09:23 PM
Post: #4
RE: Triplet Periodicity
Hey Vimal,

Thanks for making effort of building up RiboGalaxy!
I have the same issue. And the end of my sequence headers in the FASTA seems fine - they don't have any extra space but somehow I have the similar result. BTW, the FASTA file was downloaded from UCSC according to the suggestion of RiboGalaxy.

Any more suggestions?

Thanks a lot!


Yingpu
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22-Oct-2015, 09:45 AM
Post: #5
RE: Triplet Periodicity
Hi Yingpu,
It could be a problem with transcript names in the FASTA not matching with the
names in the SAM file. Could you please share your history with
ribogalaxy@gmail.com so we can investigate this further? You can do this
from the History settings -> Share or Publish and then clicking on
the "Share with a user" button.

Thanks for your interest in RiboGalaxy!

Regards,
Vimal
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22-Oct-2015, 02:59 PM
Post: #6
RE: Triplet Periodicity
Sure. Already shared, thanks!

Yingpu
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22-Oct-2015, 03:58 PM
Post: #7
RE: Triplet Periodicity
Hi Yingpu,
It appears that you had aligned the FASTQ reads to the genome and used that
alignment for riboSeqR analysis. For riboSeqR, reads should be
aligned to the transcriptome (the FASTA file you had downloaded from UCSC).
If you then rerun the Prepare riboSeqR input tool and use that output for the
Triplet periodicity step, it should work.

Please try this and let us know if you still have problems.

Regards,
Vimal
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22-Oct-2015, 04:19 PM
Post: #8
RE: Triplet Periodicity
Hey Vimal,

Trying it now, thanks for your reply!

Yingpu
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23-Oct-2015, 03:13 PM
Post: #9
RE: Triplet Periodicity
Hey Vimal,

Yeah the program went through, thanks for your help!

Yingpu


Attached File(s)
.pdf  Periodicity-plot.pdf (Size: 4.57 KB / Downloads: 10)
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29-Oct-2015, 07:40 PM
Post: #10
RE: Triplet Periodicity
I have one more question.
Is it possible to make cool figures like that?

Thanks,

Yingpu


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