Annotation question about pipernaseq

[sunyumail93]

Hi Xuan,

I am glad to hear this pipeline is useful to you. I just added more instructions about how to generate the annotation files here:
https://github.com/sunyumail93/PipeRNAseq/blob/master/preprocessing/Preprocessing.md

RefSeq.reduced.bed12.geneid.gtf is critical for building the STAR index, and it will also be used in the featureCounts step. The above preprocessing steps are mainly because the mouse RefSeq GTF file has duplicated transcripts, and I tried to keep only one copy of each. If your GTF file doesn't have duplicated transcripts (i.e., same transcript name, but occurs multiple times on different locations of the genome), you can directly rename your GTF to GENOME.RefSeq.reduced.bed12.geneid.gtf.

RefSeq.reduced.mRNA.cds.bed12.tx.STOP file is actually not used in PipeRNAseq.sh. It contains the stop codon annotation and will be used in the Ribo-seq pipeline I am developing, so you can delete or ignore it. Sorry about the confusion. I just hope different pipelines (PipeRiboseq, PipeSmRNAseq, etc) can share the GENOME folder.

If you are working on a genome that is not included in the pipeline, I am happy to help with generating the annotation. Let me know if you have any questions.

Thanks,
Yu

[xxy103]

Hi Dr. Sun,

Many thanks for your detailed explanation of the pipeline.
It is crystal clear.

Best,
Xuan

[sunyumail93]

Hi Xuan,

Thanks for the feedback. I am glad to hear that.

Thanks,
Yu