STAR alignment criteria

[Jean-Baptiste Reynier]

Hello,

We are planning to use STAR for alignment, and we noticed that in a previous version of TRUST, other requirements were indicated for the alignment : "unmapped reads are included, local alignment is disabled, number of mismatch tolerated for mapped reads should not exceed 2." Are these still valid criteria for aligned sequences used with the most recent version of TRUST?

If so, what parameters do you recommend to meet these requirements? In the supplementary material of your Nature Biotechnology correspondence, you mention two scripts for running STAR (https://media.nature.com/original/nature-assets/nbt/journal/v36/n11/extref/nbt.4294-S1.pdf). However, there is no parameter determining the maximum number of mismatches tolerated. Is the value set to 2 by default, or should we use the "--outFilterMismatchNmax" parameter?

Thank you!

J-B Reynier

[zhengy...@gmail.com]

Thank Dr. Li's kind suggestions and recommendations, STAR alignment for TRUST:

No need to add --outFilterMismatchNmax — default is fine; TRUST has overcome the mismatch number limitation

Can add --alignEndsType EndToEnd — to disable local alignment

Add --outSAMunmapped Within — to include unmapped reads

[Bo Li]

Thanks a lot for the helpful discussions!

Best,

Bo

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