---
id: "claim:kallisto-bustools-and-kb-python-for-quantifying-bulk-single-cell-and-single-nuc-2ae8ac37ce:ba8fbf9cad0ae7c6da30"
kind: "claim"
title: "kallisto bus -x <tech> -i index.idx -o output_dir -t 8 --batch-barcodes --batch batch.txt The batch.txt file looks as fo"
description: "kallisto bus -x <tech> -i index.idx -o output_dir -t 8 --batch-barcodes --batch batch.txt The batch.txt file looks as follows: batch.txt Sample1 sample1_R1.fastq.gz sample1_R2.fastq.gz Sample2 sample2_R1.fastq.gz sample2_R2.fastq.gz Sample3 sample3_R1.fastq.gz sample3_R2.fastq.gz The sample ID is in the first column. Multiple rows can be provided for the same sample ID (e.g. if the FASTQ files are divided across multiple lanes). The third column can be omitted if only one FASTQ file is specified by the technology"
url: "https://sina.bio/claim/kallisto-bus-x-tech-i-index-idx-o-output-dir-t-8-batch-barcodes-batch-b-f7664a81"
---

# kallisto bus -x <tech> -i index.idx -o output_dir -t 8 --batch-barcodes --batch batch.txt The batch.txt file looks as fo

kallisto bus -x <tech> -i index.idx -o output_dir -t 8 --batch-barcodes --batch batch.txt The batch.txt file looks as follows: batch.txt Sample1 sample1_R1.fastq.gz sample1_R2.fastq.gz Sample2 sample2_R1.fastq.gz sample2_R2.fastq.gz Sample3 sample3_R1.fastq.gz sample3_R2.fastq.gz The sample ID is in the first column. Multiple rows can be provided for the same sample ID (e.g. if the FASTQ files are divided across multiple lanes). The third column can be omitted if only one FASTQ file is specified by the technology

## Content

kallisto bus -x <tech> -i index.idx -o output_dir -t 8 --batch-barcodes --batch batch.txt The batch.txt file looks as follows: batch.txt Sample1 sample1_R1.fastq.gz sample1_R2.fastq.gz Sample2 sample2_R1.fastq.gz sample2_R2.fastq.gz Sample3 sample3_R1.fastq.gz sample3_R2.fastq.gz The sample ID is in the first column. Multiple rows can be provided for the same sample ID (e.g. if the FASTQ files are divided across multiple lanes). The third column can be omitted if only one FASTQ file is specified by the technology

## Metadata

```json
{
  "claim_position": 138,
  "source_publication_id": "version:kallisto-bustools-and-kb-python-for-quantifying-bulk-single-cell-and-single-nucleus-rna-seq--2024-10-10-nature-protocols",
  "source_work_id": "work:kallisto-bustools-and-kb-python-for-quantifying-bulk-single-cell-and-single-nucleus-rna-seq"
}
```

## Connections (1)

### kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq

- ID: `version:kallisto-bustools-and-kb-python-for-quantifying-bulk-single-cell-and-single-nucleus-rna-seq--2024-10-10-nature-protocols`
- Kind: `publication`
- Direction: `incoming`
- URL: <https://sina.bio/publication/kallisto-bustools-and-kb-python-for-quantifying-bulk-single-cell-and-si-2741fa66>

This publication contains this grounded claim.

> kallisto bus -x <tech> -i index.idx -o output_dir -t 8 --batch-barcodes --batch batch.txt Thebatch.txtfilelooksasfollows: batch.txt Sample1 sample1_R1.fastq.gz sample1_R2.fastq.gz Sample2 sample2_R1.fastq.gz sample2_R2.fastq.gz Sample3 sample3_R1.fastq.gz sample3_R2.fastq.gz ThesampleIDisinthefirstcolumn.Multiplerowscanbeprovided forthesamesampleID(e.g.,iftheFASTQfilesaredividedacross multiplelanes).ThethirdcolumncanbeomittedifonlyoneFASTQ fileisspecifiedbythetechnology.

Source: 2024-10-10-nature-protocols.pdf — <https://sina.bio/source/2024-10-10-nature-protocols-pdf>