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



The SAM or BAM file generated by user's aligner. We require this file contains the header section. If input is a SAM file, it must end with suffix 'sam' (case insensitive). If input is a BAM file, it must end with suffix 'bam' (case insensitive).


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


-T/--temporary-directory <directory>

'convert-sam-for-rsem' will call 'sort' command and this is the '-T/--temporary-directory' option of 'sort' command. The following is the description from 'sort' : "use DIR for temporaries, not $TMPDIR or /tmp; multiple options specify multiple directories".


Show help information.


This program converts the SAM/BAM 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. This program will create a temporary directory called 'output_file_name.bam.temp' to store the intermediate files. The directory will be deleted automatically after the conversion. 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 file is valid.

Note: This program does not check the correctness of input file. You should make sure the input is a valid SAM/BAM format file.


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.