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Request for xpore result of HEK293T-rep2 #160
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Hi @kwonej0617, Sorry for the delayed reply! Here is the link to the HEK293T-WT-rep2 and HEK293T-Mettl3-KO-rep2 we generated: Thanks! Best wishes, |
@yuukiiwa Thank you for your data! Also, I have a question regarding minimap usage. Thank you for your help! |
Hi @kwonej0617, Here is the command for preparing an
Then, the alignment command looks like the following:
I know people who run the indexing step and the alignment step of Thanks! Best wishes, |
Hi, @yuukiiwa
In terms of minimap2, minimap2.1 was mentioned in the paper. Did it mean this version Minimap2-2.1 (r311) https://github.com/lh3/minimap2/releases/tag/v2.1? |
Hi @kwonej0617, Yes, the Best wishes, |
Thank you so much @yuukiiwa ! |
Hi, would you mind sharing the reference file you used when running minimap2? It would be also very helpful if you could how I made my reference file. Thanks for your help! |
I found a file "Homo_sapiens.GRCh38.cdna.ncrna_wtChrIs_modified.fa" https://zenodo.org/record/5707193#.Y3rL9n1Bw2w. Did you use it as your reference .fa file? It would be very helpful if you could share the reference file and annotation file used in your analysis. Thank you so much! Happy new year. |
Hi @kwonej0617, Happy New Year to you too! (sorry for the delayed reply) Yes, we used Thanks! Best wishes, |
Thank you, @yuukiiwa ! |
Hi @yuukiiwa I really appreciate your help so far. - Guppy
All fastq files were combined with cat command after guppy was finished. - Generating the mmi file for alignment
- Alignment with minimap2 (minimap2/2.1.1, samtools/1.16.1)
The generated sam file looks like, - Nanopolish (nanopolish/0.13.3)
The eventalign file looks like, - xPore dataprep (xpore/2.1)
Dataprep otuput looks like succssfully generated. I run the same steps for HEK293T-WT-rep2 and Mettle3-rep2 data. - xPore diffmod (xpore/2.1)
diffmod.log
Also, even same m6A sites have different stats between two data.
I really appreciate your help! |
Hi @kwonej0617, Sorry for the delayed reply! The difference is probably due to the different versions of the guppy used. We used guppy 2.1.3 instead of 6.0.7. Thanks! Best wishes, |
Hi, @yuukiiwa Lastly, could you provide me kit # and flowcell for samples as follows? Thank you! |
Hi @kwonej0617, @ploy-np used Your commands look fine to me. Here is the information on the FLO cell ID and sequencing kit for the samples: Thanks! Best wishes, |
Hi, @yuukiiwa I really appreciate your quick response! |
Hi, @yuukiiwa. I really want to replicate supplementary data1. So I performed preprocessing steps, guppy, minimap2, nanopolish and xPore with HEK293T-WT/KO-rep1,2,3 using the command lines in my previous comments posted 3 weeks ago, which is based on xPore manual documentation. Then, I compared my result to supplementary data1. I really appreciate your help! |
Hi @kwonej0617, It is not up to us to distribute any version of Best wishes, |
Hi @yuukiiwa Thank you for your response! I understand that. I really appreciate your help! |
Hi @kwonej0617, Sorry for the delayed reply! I was on vacation last week. I don't think using different versions of Thanks! Best wishes, |
Hi, @yuukiiwa Thanks for your reply! Also, hope you had a great vacation! :) Thank you so much! |
Hi, developer.
Thank you for providing a useful tool!
I have run xpore and generated the result with HEK293T-WT-rep2 and HEK293T-Mettl3-KO-rep2 successfully.
I wanted to check whether I correctly generated the input files for xpore and run xpore by comparing my result with yours.
Could you share the raw xpore result of HEK293T-WT-rep2 (KO vs. WT)?
Thank you so much!
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