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During the pre-processing of the pileup file, variants like the one below are removed:
`chr11 35208126 T 49 ccc,CCCCc,C,>
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There are a number of features that we'd like to support that require knowing how wide a layout is:
- `\overbrace`, `\underbrace`
- `\cancel`
- `\overrightarrow`, `\overleftarrow`
- `\widehat`, `\…
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# Lexical Schemas
### The Problem
A lot of mistakes with Lexical are caused by developers adding nodes where they shouldn’t.
Schemas are an API proposal that’s designed to add guardrails aro…
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I used scNanoGPS to analyze Nanopore data with 10X Visium cDNA. The results looked good However I have a few questions about the Minimap2 aligner and what parameter to use
The scNanoGPS pipeline by …
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Sample
```
SJ000026/SJRHB026_S ngs_pipeline_SJ000026=SJRHB026_S=20220911
```
Error
```
/data/khanlab2/processed_DATA/ngs_pipeline_SJ000026=SJRHB026_S=20220911_20221220_005858.log
Error in rul…
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Hi
I have been trying for 3 days but still coulnd't get it work on my end. Sorry I have very little knowledge and training in bioinformatics so please bear with me with the basics. I had RNA-seq da…
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Hello syncmer_mapping team,
I noticed that the modified minimap2 (syncmer), minimizer window size is now 0, but several options related to minimizer are still there (e.g., minimal number of minimiz…
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Hi @andrewprzh , based on a previous issue I understand that:
`OUT.transcript_counts.tsv` contains count of all known transcripts
`OUT.transcript_model_counts.tsv` contains counts of all novel t…
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Hello,
I have three replicates of ONT cDNA sequencing files. A lot reads of them have assigned to a lnc gene, but the gene counts in one sample was zero. Why it happens ?
![image](https://github.…
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~/src/modPhred/run -f ./reference_genome_files/GRCh38.p13.genome.fa -o ./combined_sh33/ -i ./workspace/
[2024-02-22 14:41:06] ===== Welcome, welcome to modPhred pipeline! =====
[2024-02-22 14:41:06]…