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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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Can I use existing alignment results from STAR as input for LIONS? #27

Closed Lynuxoo closed 1 year ago

Lynuxoo commented 1 year ago

Hello,

I noticed that LIONS uses TopHat for alignment. Now that I have the alignment results from STAR, is there a way to provide my existing alignment results as input to LIONS?

Thanks in advance for your help!

ababaian commented 1 year ago

Yes, in the parameter file there is a an ALIGNMENT BYPASS flag which you can set to use bam files as they are provided.

See: https://github.com/ababaian/LIONS/blob/595bc6fc2a8f6d2f31ce121d63a9d3a7a812af6e/controls/parameter.ctrl#L55

Cheers