---
name: "convert-sam-for-rsem"
section: "1"
platform: "linux"
package: "rsem"
version: "1.3.3+dfsg-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/convert-sam-for-rsem"
---

# convert-sam-for-rsem(1)

Make a RSEM compatible BAM file.

## NAME

convert-sam-for-rsem - Make a RSEM compatible BAM file.

## SYNOPSIS

```
 convert-sam-for-rsem [options] <input.sam/input.bam/input.cram> output_file_name
```

## ARGUMENTS

- **input.sam/input.bam/input.cram**

  The SAM/BAM/CRAM file generated by user's aligner. We require this file contains the header section.

- **output\_file\_name**

  The output name for the converted file. 'convert-sam-for-rsem' will output a BAM with the name 'output\_file\_name.bam'.

## OPTIONS

- **-p/--num-threads** \<int\>

  Set the number of threads to be used for converting. (Default: 1)

- **--memory-per-thread** \<string\>

  Set the maximum allowable memory per thread. \<string\> represents the memory and accepts suffices 'K/M/G'. (Default: 1G)

- **-h/--help**

  Show help information.

## DESCRIPTION

This program converts the SAM/BAM/CRAM file generated by user's aligner into a BAM file which RSEM can process. However, users should make sure their aligners use 'reference\_name.idx.fa' generated by 'rsem-prepare-reference' as their references and output header sections. After the conversion, this program will call 'rsem-sam-validator' to validate the resulting BAM file.

Note: You do not need to run this script if \`rsem-sam-validator' reports that your SAM/BAM/CRAM file is valid.

## EXAMPLES

Suppose input is set to 'input.sam' and output file name is "output"

```
 convert-sam-for-rsem input.sam output
```

We will get a file called 'output.bam' as output.