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#### What analysis module should be updated and why?
Running the `sex-prediction-from-RNA-seq` module with the v13 kallisto data lead to the loss of feature names due to #474.
#### What cha…
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Dear Pachter Lab members,
There is a single-cell method named [haircut-seq](https://academic.oup.com/nar/article/doi/10.1093/nar/gkaa240/5819935) which I'm trying to reimplement their pipeline usi…
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proposed topic: RNAseq. Kallisto paper, anyone?
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The page https://pachterlab.github.io/kallisto/starting says "we have placed some transcriptome fasta files for human and model organisms here", linking to http://pachterlab.github.io/kallisto/transcr…
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I have 10X 3' v1 chemistry data with four fastq files:
```
EBT0_1A_S1_L001_I1_001.fastq.gz # 8 nt per read
EBT0_1A_S1_L001_R1_001.fastq.gz # 98 nt per read
EBT0_1A_S1_L001_R2_001.fastq.gz # 16 n…
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from @tkphd
Conda is a common and useful tool, but it is simply invoked, not
introduced. Explain what it is (a Python distribution with virtual environment
isolation), how it helps (simplifies de…
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Hi there!
Thanks for developing this awesome tool! I am currently using kallisto-bustools to generate single-cell equivalence class counts.
I am wondering if there is a way of **linking an equiva…
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Hi!
I have run kallisto on RNA-Seq data from SRA. Unfortunately, it does not have any replicates. After kallisto, I try to run sleuth with recommended commands (https://pachterlab.github.io/sleuth_…
gezmi updated
6 years ago
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Hello,
I am executing
```
kallisto quant -t 8 -i local_kallisto_index_file -o local_folder_align_out file_name_1 file_name_2
```
for large number of samples on cloud machine. After every…
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When trying to get pesudobam file, it gives me the core-dump error.
Machine is Ubuntu server with x86-64 architecture.
```
kallisto quant -i Trinity.fasta.kallisto_idx -l 590 -s 160.95 -o out --pseu…