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Producing transcriptomic bam with STAR with all sam attributes
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19 months ago
rubic • 180
United States

Perhaps someone here knows how to get STAR to produce, in addition to the genomic bam output, a transcriptomic bam output, which includes all sam attributes.

I'm running STAR 2.5.2a like this:

STAR --runMode alignReads --readFilesCommand zcat --runThreadN 8 --genomeDir <dir> --readFilesIn <fastq.gz.1> <fastq.gz.2> --outSAMprimaryFlag AllBestScore --outFilterMismatchNoverLmax 0.05 --limitSjdbInsertNsj 4339995 --outFilterIntronMotifs RemoveNoncanonical --quantMode TranscriptomeSAM --quantTranscriptomeBan Singleend --outSAMattributes All --outSAMstrandField intronMotif --sjdbFileChrStartEnd <space_delimited_list_of SJ_files_from_first_STAR_run> --outSAMtype BAM Unsorted --outFileNamePrefix <output_prefix>

This means I've already ran a first STAR pass and am now running a second pass giving it all SJ files from the first pass, but that's really not the point here.

The point of the question is that while the genomic bam output (output_prefix.Aligned.out.bam) produces all sam attributes:

NH, HI, AS, nM, NM, MD, jM, and jI

Since I specified: --outSAMattributes All

The transcriptomic bam (output_prefix.Aligned.toTranscriptome.out.bam) only has: NH and HI

Not having NM causes MMSEQ, which I feeding with the transcriptomic bam to crash with a segmentation fault since it's assuming NM is there.

So, any what's the deal and how to get STAR to output all sam attributes in the transcriptomic bam?

RNA-Seq STAR • 978 views

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