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xryanglab / RiboCode

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Whether multiple mapping affect ribocode result #42

Open Hilarialy opened 2 years ago

Hilarialy commented 2 years ago

Sorry to bother you. I followed your workflow use STAR arguments --quantMode TranscriptomeSAM and --outFilterMultimapNmax 1,this is the command looks like

STAR --outFilterType BySJout --runThreadN 10 --outFilterMismatchNmax 2 \
--genomeDir /reference/GRCm38/STAR \
--readFilesIn /my/rmrRNA/${sample}_trim_norrna.fq  \
--outFileNamePrefix ${sample} \
--outSAMtype BAM SortedByCoordinate \
--quantMode TranscriptomeSAM GeneCounts \
--outFilterMultimapNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd

the output Aligned.toTranscriptome.out.bam file still have multiple mapping sequence ( NH:i > 1 ) , because STAR wiil output all records in this toTranscriptome bam file , Does these multiple mapping records affect the Ribocode result to find uORF ?

zhengtaoxiao commented 2 years ago

STAR excludes those reads aligned to multiple genome regions, not the transcriptome. It is expected to see "NH:i>1" in transcritome bam file for those genes having multiple overlapped isoforms. It has no influence on RiboCode result.