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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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Linuxにて作業をしています。
下記のように、104ページのkallistoの出力ファイルを読み込むを実行しました。
> so
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Hi I am pretty new to kallisto/bustools so thank you for your help in advance. I followed directions from this issue/Google collab: [Issue #75](https://github.com/BUStools/bustools/issues/75)
I ra…
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Hello,
I am trying to create index for "Homo_sapiens.GRCh38.dna.primary_assembly.fa" from Ensembl. I installed Kallisto using conda (kallisto 0.48.0) and tried to index using `kallisto index -i Homo_…
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Hi, I am using the following command to make the index file. However, I am getting an ERROR.
./kallisto index -i /DataAnalysis/kallisto_test/transcripts.idx /DataAnalysis/kallisto_test/Homo_sapien…
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Hi all,
I am using kallisto with this command:
kallisto quant -i kallisto_index --bias --genomebam --chromosomes chrm.sizes.txt --gtf ITAG3.10_gene_models.gtf -o test R2_001.tr.fq.gz R2_001.tr.fq…
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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,…
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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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ENHANCEMENT:
I'd like to be able to use kallisto as such:
```
seqtk mergepe read1.fq read2.fq | skewer | kallisto quant -i -
```
basically, moving from raw reads, through adapter trimming, to kalli…
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I have followed https://pachterlab.github.io/kallisto/source guide to build Kallisto on a 11.2.3 macOS Big Sur, doing the following steps:
```
# install Homebrew package manager
% /usr/bin/ruby …