Bacterial Transcriptome alignment using STAR

[Madhura Tathode]

Hi All,

I need help regarding using STAR aligner for Reference guided - Bacterial transcriptome alignment (Organism: Lactobacillus).

STAR is mainly Splice aligner and used for larger genome alignments. However, it is also used for smaller genome alignment including bacteria (which does not have splice variants).  

I want to use STAR for Lactobacillus transcriptome assembly and interested in knowing specific parameters which needs to be considered while aligning the reads to bacterial genome/transcriptome? Could you please help me in this? 

Here are sequencing details:

1) Paired end reads with 75 bp read length.

2) Minimum of 30 million reads per sample (Total no. of samples: 12).

Looking forward to hearing from you.

Thank you.

[Alexander Dobin]

Hi,

the standard mapping parameters will work.

You may want to prohibit splicing with --alignIntronMax 1