rRNADepletion

This repository contains scripts used to generate probe sequences for rRNA depletion.

These scripts were used in our manuscript:

Gu, H., Sun, Y.H. and Li, X.Z., 2021. Novel rRNA-depletion methods for total RNA sequencing and ribosome profiling developed for avian species. Poultry Science

Usage

1, Download and set up scripts

git clone https://github.com/LiLabZhaohua/rRNADepletion.git
cd rRNADepletion && chmod +x *py

2, Convert FASTA files to one-line FASTA:

./FastaSeqLinearizer.py Original_Sequence/Gallus_12S_rRNA_mitochondria_MH879470_Complete.fa Gallus_12S.fa
./FastaSeqLinearizer.py Original_Sequence/Gallus_16S_rRNA_mitochondria_MH879470_Complete.fa Gallus_16S.fa
./FastaSeqLinearizer.py Original_Sequence/Gallus_18S_rRNA_AF173612.1.fa Gallus_18S.fa
./FastaSeqLinearizer.py Original_Sequence/Gallus_28S_rRNA_XR_003078040.1.fa Gallus_28S.fa
./FastaSeqLinearizer.py Original_Sequence/Gallus_5.8S_rRNA_XR_003078039.1.fa Gallus_5.8S.fa
./FastaSeqLinearizer.py Original_Sequence/Gallus_5S_rRNA_XR_003076910.1.fa Gallus_5S.fa

3, Generate probe sequences

./RiboProbeGenerator.py Gallus_12S.fa Gallus_12S.probes.fa
./RiboProbeGenerator.py Gallus_16S.fa Gallus_16S.probes.fa
./RiboProbeGenerator.py Gallus_18S.fa Gallus_18S.probes.fa
./RiboProbeGenerator.py Gallus_28S.fa Gallus_28S.probes.fa
./RiboProbeGenerator.py Gallus_5.8S.fa Gallus_5.8S.probes.fa
./RiboProbeGenerator.py Gallus_5S.fa Gallus_5S.probes.fa

4, Remove multi-mapping probe sequences using UCSC BLAT against galGal6 chicken genome:

UCSC genome browser for galGal6

UCSC BLAT for galGal6