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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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LIONS for stranded RNA-Seq data #24

Open rpg18 opened 3 years ago

rpg18 commented 3 years ago

Hi! Can LIONS identify the library type of the data set? I realised that RNAseqPipeline.sh script uses the strand information of the reads to generate the expression wig files. However, while in the code the parameter sr equal to "S" determines stranded, it is fixed the "R" option - see eastLion.sh here. How will this affect the final output for stranded RNA-Seq data? Should it be necessary to include the sr parameter in parameter.ctrl script here?

Additionally, among Cufflinks parameters, the -library-type parameter is missing in parameter.ctrl and in eastLion.sh. How can Cufflinks identify the library type without the -library-type parameter if the input bam files where generated with STAR including the XS tag, for example?

Thank you in advance. Cheers!

ababaian commented 3 years ago

That's kind of a carry-over from earlier work. If you're doing cufflinks assembly then the strand information is kind of redundant since splice junctions will tell you which strand the assembly is from. There are some edge-cases here with bi-directional promoters but I just accepted it as a source of error since most of my data was not stranded. There is not good strand-support at this time :)

rpg18 commented 3 years ago

Thanks for the prompt reply! I tried to run LIONS with STAR mapped reads and Stringtie assemblies, selecting the strand-specific modality with the sr parameter, such as sr="S". By doing this, "Error 12" appears because a final wig file for each sample is not generated, instead only the positive and negative wig files are generated. At this point, would you recommend to run LIONS' default regular-paired-end modality, such as sr="R", accepting this strandness limitation?

Thank you again ;)

ababaian commented 3 years ago

That makes sense, I would for sure just run it with the default in that case and the data you have, it should make single wig files and hopefully that works. :crossed_fingers: