convert-sam-for-rsem [options] <input.sam/input.bam/input.cram> output_file_name
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.
convert-sam-for-rsemwill output a BAM with the name 'output_file_name.bam'.
sortcommand and this is the -T/--temporary-directory option of
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.