Missing parameter for Stringtie if use STAR as alignor

[xianggenti]

Description of the bug

Ref: https://github.com/gpertea/stringtie Missing XS tag from STAR.

bam file Header: @PG ID:STAR PN:STAR VN:STAR_2.6.1d CL:STAR --runThreadN 12 --runRNGseed 0 --genomeDir STARIndex --readFilesIn EngTreg2_1_1_val_1.fq.gz EngTreg2_1_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix EngTreg2_1. --outSAMtype BAM Unsorted --outSAMattributes NH HI AS NM MD --outSAMattrRGline ID:EngTreg2_1 SM:EngTreg2_1 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --sjdbGTFfile genes.gtf --quantMode TranscriptomeSAM --quantTranscriptomeBan Singleend --twopassMode Basic

Quote from Stringtie: "Any SAM record with a spliced alignment (i.e. having a read alignment across at least one junction) should have the XS tag to indicate the transcription strand, i.e. the genomic strand from which the RNA that produced this read originated. TopHat and HISAT2 alignments already include this tag, but if you use a different read mapper you should check that this tag is also included for spliced alignment records. STAR aligner should be run with the option --outSAMstrandField intronMotif in order to generate this tag."

Command used and terminal output

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Relevant files

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System information

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