1. Local or EndToEnd

Using --alignEndsType EndToEnd , which requires end-to-end alignment for each read (no soft clipping). This might be too harsh for longer reads, which are more likely to have poor quality tails, adapters at the ends etc. Please try to map without this option。

ref1: http://seqanswers.com/forums/showthread.php?t=27470&page=11

ref2: https://github.com/alexdobin/STAR/issues/455

HISAT2

<font style="color:#383838;background-color:rgba(221, 221, 221, 0.1);">--no-softclip</font>

2. <font style="color:rgba(0, 0, 0, 0.87);">seedSearchStartLmax</font>For shorter reads

对于长度有异质性的测序数据来说<font style="color:#500050;">--seedSearchStartLmaxOverLread </font> set to 0.5 to account for variable ribosome footprint lengths.

ref1: The Translational Landscape of the Human Heart (method)

key parameters: 但是我在实践过程中发现，许多数据减小参数<font style="color:rgba(0, 0, 0, 0.87);">--seedSearchStartLmax</font>并不会增加短reads的mapping率，这也是让STAR作者思考的一个问题。

ref1: https://groups.google.com/g/rna-star/c/_SXz370eyVA?pli=1