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1. webscraping_api
- plant cyc
- SRA
- ENA
- ChatGPT?
2. data-parsing
- fasta manipulation. read / write fasta files. Removing sequences based on SeqID. Retaining primary transcripts based on…
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Salmon output depends on random numbers. The random number generator seeds cannot be set by the user:
https://github.com/COMBINE-lab/salmon/issues/185
Kallisto would be a viable alternative…
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kallisto version 48.0
OS: macOS Monterey Version 12.6.5
Issue: Unable to compile kallisto with -DUSE_HDF5=ON, kallisto ignores bootstrap option.
kallisto returns:
```
Warning: kallisto was no…
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I am using 0.46.1 under WSL 2 Linux 64bits with 32Gb RAM memory
By using a 346Mb fasta.gz file, I get a std::bad_alloc error
And..
If a decompress the file to its 1.24Gb fasta file, the index is'…
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I am trying to run the kallisto quant command on a machine with limited resources.
Processor: Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz 2.90 GHz
RAM: 20.0 GB (19.9 GB usable)
I don't care if…
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Hello,
currently, I am trying to run IsoformSwitchAnaylzer with Kallisto counts. After successfully using importIsoformExpression() to extract my count data, I wanted to set up the switchAnalyzeRlis…
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Why is there a big difference between kallisto and cellranger count result?
sample:
https://www.ncbi.nlm.nih.gov/sra/SRR8315735
kallisto:
![image](https://user-images.githubusercontent.com/3…
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Hello Everybody,
I perform single cell sequencing using droplet microfluidics and barcode cells using barcoded hydrogel beads generated by split and pool technique.
The structure of my library is:
…
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Here is what the nextflow version is currently outputting in a transXpress_results folder in the working directory of the pipeline execution (using rnaSPAdes as an example):
```
0226_Chattonella_sub…
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I am trying to re-process the [data from Grun et al 2016](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2142263) (a CEL-Seq paper), and I am getting very low counts from kallisto and bustools,…