lauraht

Is it possible to add a “--shortname" option for isONclust to output the read name with “the read id only”?

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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...

Is it possible to use isONclust to help determine whether two reads came from the same isoform?

15

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...

An issue with the installation/environment

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Hello! I have an issue with the isONcorrect installation and would appreciate your advice. Last November, I installed isONcorrect using conda (and created the isoncorrect env) by following your README...

Question about matching minimizers in all-vs-all overlaps of ONT RNA-seq reads

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Hi Heng, I use the `-x ava-ont` option in minimap2 to get all-vs-all overlaps of ONT RNA-seq reads. I also output the matching minimizers’ positions in each read for a...

Can we use pychopper to trim all the reads including non-full-length reads?

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Hello! I have cDNA and direct RNA Nanopore reads which contain poly-A/poly-T sequences and adapters/barcodes. A friend suggested me to use pychopper to remove those poly-A/poly-T sequences and adapters/barcodes. I...

StringTie dealing with the read alignments which do not have the XS tag

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Hi Geo, In my BAM file, there is a certain number of spliced read alignments which do not have the XS tag. My understanding is StringTie will ignore those spliced...

Hello! I was reading the PBSIM readme page and have a question regarding the following description: ``` To run model-based simulation: pbsim --data-type CLR --depth 20 --model_qc data/model_qc_clr sample/sample.fasta In...

Keras/tensorflow failed when specifying class_weight in model.fit()

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**System information**. - OS Platform and Distribution: Linux. - TensorFlow version: Keras/tensorflow version 2.8.0. - Python version: Python 3.7 - GPU model and memory: Use CPU (no GPU). **Describe the...