This repository contains the custom scripts used in the following manuscript:
"Identification of sheep lncRNAs related to the immune response to vaccines and aluminium adjuvants. BMC Genomics 22, 770 (2021). https://doi.org/10.1186/s12864-021-08086-z "
Note that the scripts are not optimized and may be slow.
RNA-seq and small RNA-seq data analised in this work can be found here: GSE113899
- filter2_pbmc.py: Executable script to filter the gffcompare output for novel potential lncRNAs.
filter2_pbmc.py [gffcompare.gtf] [outdir]
- translate3frames.py: Executable script to translate sequences in the 3 possible frames.
translate3frames.py [dna_sequences.fa] [output.fa]
- classification_lncrnas.py: Executable script to classify lncRNAs by location to nearest gene. The pybedtools suite is necessary.
classification_lncrnas.py [lncrna_list.txt] [gffcompare.gtf] [ensembl.gtf] [outdir]
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ens_blast.py: Code used for sequence conservation analysis of novel sheep lncRNAs and Ensembl lncRNAs. Biopython and standalone NCBI Blast are necessary.
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synteny_noncode.py: Code used for syntenic conservation analysis of novel sheep lncRNAs and NONCODE cow lncRNAs. Biopython is necessary.
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synteny_ens.py: Code used for syntenic conservation analysis of novel sheep lncRNAs and Ensembl lncRNAs. Biopython is necessary.
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closegenes_isoforms_pbmc.py: Code used to perform correlations between lncRNAs and close genes.