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STAR ENCODE option

Hi,

I am using STAR to align my RNA-seq data. I found in ENCODE options: the max number of multiple alignments allowed for a read is 20 (i.e. --outFilterMultimapNmax 20). Why it was not set as 1 to include only unique mapped reads for downstream analysis?

Thanks! Lei

rna-seq
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updated by Biostar Biostar • written by tianleivv • tianleivv

1 answer

Because counting tools such as featureCounts and HTSeq can exclude multi-mapping reads, and other tools such as RSEM and eXpress can use the information from multi-mapped reads to provide more accurate count estimates.

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written by h.mon h.mon

Thanks h.mon! Why did you say RSEM can use the information from multi-mapped reads to provide more accurate count estimates? Do you have any references for this?

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written by tianleivv • tianleivv

RSEM paper. Read the section "Transcript quantification" from the review A survey of best practices for RNA-seq data analysis for a better explanation of the differences between aggregated raw counts (HTSeq and featureCounts) versus expectation-maximization estimated counts (RSEM, eXpress and Salmon).

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written by h.mon h.mon

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