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Weeks-UNC / shapemapper2

Public repository for ShapeMapper 2 releases
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Output reactivity for entire transcriptome #47

Open reislab opened 1 year ago

reislab commented 1 year ago

Hello, We've produced in vivo probing data (SHAPE treated and untreated) to study transcriptomic structures, but shapemapper2 doesn't natively output reactivity data for entire transcriptome. We've tried the solutions given in FAQ (Can I run ShapeMapper on multiple RNAs at the same time?), but no success so far. Our current version is shapemapper-2.1.4, in case that matters. Would you have a detailed reference (e.g., published paper or script) that shows how to use shapemapper2 with transcriptome? We found a preprint that did just that (10.1101/2023.05.09.540021), but the scripts/method might come only with the peer-reviewed article. Many thanks, Rodrigo

m-Mueller-m commented 1 year ago

Hi, we have the same issue and would really appreciate a detailed documentation to run ShapeMapper2 on the whole transcriptome (in our case in DMS mode). Many Thanks, Mara

Psirving commented 1 year ago

Hi Mara and Rodrigo,

We have our own unpublished pipeline, but the grad student working on that is currently out of town. I know that he uses a modified version of shapemapper-txome. I will get more detail for you when he returns.

I actually don't know the details of how our collaborators in the Dong lab acheived their transcriptome-wide analysis (the paper Rodrigo mentioned). I will reach out to them.

Just in case, @anthonymustoe, do you have a solution to this?

anthonymustoe commented 1 year ago

Hi Patrick et al,

No, we don't have an alternative solution. Sorry.

Tony

On Wed, Aug 16, 2023 at 12:17 PM Patrick Irving @.***> wrote:

Hi Mara and Rodrigo,

We have our own unpublished pipeline, but the grad student working on that is currently out of town. I know that he uses a modified version of shapemapper-txome https://github.com/Weeks-UNC/shapemapper-txome. I will get more detail for you when he returns.

I actually don't know the details of how our collaborators in the Dong lab acheived their transcriptome-wide analysis (the paper Rodrigo mentioned). I will reach out to them.

Just in case, @anthonymustoe https://github.com/anthonymustoe, do you have a solution to this?

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davidqiu54 commented 11 months ago

Hi there, sorry for the very late response but I hope this is still helpful. The modified version of shapemapper-txome that I used is attached to this comment. Do note that all the dependencies for shapmapper-txome are still required for this version to work. You can read the shapemapper-txome documentation to know the required dependencies there are and what each of the commands do.

Its use is rather simple, the only required input files are a fasta file with all of the sequences you wish to align to and of course fastq sequencing read files. Full transcriptome fasta files are pretty easy to find, with the MANE annotation being an example for the human transcriptome. You will also probably need a very powerful processing unit to handle all the alignments.

shapemapper-txome.zip