issues Search Results · repo:ksahlin/isONclust language:Python
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inksahlin/isONclust (press backspace or delete to remove)Hello, Firstly, thank you for the package! We are currently trying the tool for our transcriptomic data set. The tool
works perfectly fine in clustering mode but we encountered an error when extracting ...
NHoang98
- 9
- Opened on Sep 4, 2024
- #25
Hello! Thank you for the tool. I run it with some samples, and the results are promising. Currently, I am testing this
tool for one pipeline that should handle many ONT barcoded samples. I have already ...
timyerg
- 7
- Opened on May 17, 2024
- #24
I was using isONclust in parallel as a previous step to define a transcriptome using ONT data with isONform. I looked at
the memory profiling of isONclust and after a few minutes, when almost reaching ...
eprdz
- 8
- Opened on Dec 21, 2023
- #23
Hi! I am working with samples from nanopore. I successfully used isOnclust on a single sample, but I would need to
compare various samples. Is it possible to use isOnclust on multiple samples?
ghost
- 4
- Opened on Aug 19, 2022
- #22
Hi I am running isONclust in a Conda environment and the spoa and medaka modules are loaded before the run.
Here is my commands:
ml Miniconda3/4.10.3
source activate isonclust
ml spoa/4.0.0-GCC-8.3.0 ...
Malabady
- 2
- Opened on Mar 9, 2022
- #21
Hello!
I have a question regarding the read order in each cluster in the final_clusters.tsv file and would appreciate your
advice.
My understanding is that isONclust first sorts the reads such that longer ...
question
lauraht
- 6
- Opened on Feb 15, 2022
- #20
Thanks @ksahlin for the great tool. I ve been trying to use for a variety of clustering tasks using some amplicon data.
I still have some uncertainty on how it is performing as I don t necessarily know ...
nextgenusfs
- 4
- Opened on Dec 7, 2021
- #19
Hi Kristoffer,
I was wondering if it would be possible to add a --shortname option for isONclust to output the read name with “the read
id only” instead of the entire @ line (currently the entire @ line ...
- 1
- Opened on Oct 21, 2021
- #18
Hi Kristoffer,
I understand that each cluster generated by isONclust represents all reads that came from the same gene.
However, I was looking for a de novo tool/method that could determine whether two ...
- 15
- Opened on Oct 11, 2021
- #17
I am getting this error within the multiprocessing.pool.RemoteTraceback library. I am running the following command
isONclust \
--ont \
--fastq results/.temp/merged.barcode.clusters.fastq \
--q 7 \
--aligned_threshold ...
JoshLoecker
- 8
- Opened on Mar 26, 2021
- #16
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