Does RSEM need HI:i:<n> tag to correctly process multimappers? about rsem HOT 2 OPEN

Yes, RSEM does require the HI:i: tag in order to correctly process multimappers. The HI tag (HI:i:) is a field in SAM/BAM files that is used to indicate the index of a read within the input file. When processing multimapped reads, RSEM uses the HI tag to keep track of which reads are duplicates, so that they are not counted multiple times.

If the BAM files generated by Hisat2 do not contain the HI tag, you can add it using the samtools command-line tool. The samtools addreplacerg command allows you to add or modify the values of any field in the SAM/BAM header, including the HI tag.

Here's an example of how to add the HI tag to a BAM file using samtools:

samtools addreplacerg -r 'ID:1' -r 'SM:sample' -r 'PL:illumina' -r 'PU:unit' -r 'LB:library' -r 'DT:2023-05-03T12:34:56-0700' -R 'HiSeq2500' -i 'HI' -o output.bam input.bam

In this example, the ID, SM, PL, PU, LB, and DT tags are arbitrary and can be changed to match your specific sample information. The -R option specifies the sequencing platform used to generate the data, and the -i option specifies the name of the index tag to be added (in this case, "HI"). The input BAM file is "input.bam", and the output BAM file with the added HI tag is "output.bam".

from rsem.

Hi Aryan,

Thank you for your answer! I am confused, however. RSEM appears to support hisat2 as a mapping tool - yet the options used by RSEM do not allow for HI tag to be outputted.

The issue I was having was due to sorting of the BAM file; apparently, transcriptomic files are always read name-sorted by default, and both RSEM and Salmon expect this to be true in order to work correctly. Adding HI tag does not seem to influence the result.

from rsem.