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Creating this ticket to evaluate a lighter weight pipeline using [Kallisto](https://pachterlab.github.io/kallisto/) for quantification.
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I am testing our usual quantification pipelines with `kallisto` and `bustools`, and noticed `bustools capture` seems to have problem with its barcode mode, if the barcodes are long (in this case, 38bp…
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I know kallisto works with the transcriptome and not genome.
As you don't have the indexed genome for Drosophila yet for the newer version of kallisto I would like to create it myself.
I was w…
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WIth typical kallisto pseudoalignment rates of ~70% for human total ribo-depleted RNA libraries, an obvious question is what the remaining 30% of reads represent, especially when aligners like hisat2 …
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Hi,
I got the following error message from kallisto quant, but kallisto seems to be on version 0.50.0 and it doesn't explain what those versions refer to.
```
[quant] fragment length distributio…
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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…
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i run kallisto on ubuntu 20.04 it produce three output files, but when i run kallisto on mac it produce only two files, h5 file missing. sharing commond line used in this operation
![Screenshot from …
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学生です。教本でNGS解析の勉強をしています。
kallistoとsleuthの処理を行っているのですが、
104ページのkallistoの出力ファイルを読み込む、のコマンドを入力したところ、
In check_target_mapping(tmp_names, target_mapping) :
intersection between target_id from kallis…
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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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sample:
https://www.ncbi.nlm.nih.gov/sra/SRR8315735
kallisto result:
![image](https://user-images.githubusercontent.com/3069871/219325395-4fc16c91-4d2d-423f-90dc-f6f3ce4aef62.png)
cellranger r…