MinION_Transcriptome

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes
Studying bacterial transcriptomes using RNA-seq
start with tailfinder, make sure if the information given in the data summaries are correct. (especially direct RNA sequencing, is it polyA tailed?)

Name		Name	Last commit message	Last commit date
Latest commit History 78 Commits
.vscode		.vscode
TAMA_scripts		TAMA_scripts
TU_annotation		TU_annotation
bam_parse		bam_parse
post_transcription		post_transcription
pre_process		pre_process
scripts		scripts
.DS_Store		.DS_Store
.Rhistory		.Rhistory
16S_analysis.Rmd		16S_analysis.Rmd
Copenhageni.sqlite		Copenhageni.sqlite
GCF_000007685.1_ASM768v1_genomic.sqlite		GCF_000007685.1_ASM768v1_genomic.sqlite
README.md		README.md
TAMA_analysis.Rmd		TAMA_analysis.Rmd
cDNA_Salmon_quant.Rmd		cDNA_Salmon_quant.Rmd
cDNA_map_stats.Rmd		cDNA_map_stats.Rmd
centrifuge.analysis.Rmd		centrifuge.analysis.Rmd
dRNA2_map_stats.Rmd		dRNA2_map_stats.Rmd
get_ORF_with_TSS_TTS.py		get_ORF_with_TSS_TTS.py
gtdbtk.analysis.Rmd		gtdbtk.analysis.Rmd
homopolymer_cov.Rmd		homopolymer_cov.Rmd
kraken2.minION.Rmd		kraken2.minION.Rmd
mapping_stats_analysis.Rmd		mapping_stats_analysis.Rmd
minION_polyA_analysis.Rmd		minION_polyA_analysis.Rmd
salmon_analysis.Rmd		salmon_analysis.Rmd
salmon_tx2gene_convert.sh		salmon_tx2gene_convert.sh
stringtie_analysis.Rmd		stringtie_analysis.Rmd
sub.sh		sub.sh
submit_pipeline-polya-ng.sh		submit_pipeline-polya-ng.sh
tailfindr.analysis.Rmd		tailfindr.analysis.Rmd
test.tab		test.tab
test1.tab		test1.tab
tts_annotate.Rmd		tts_annotate.Rmd
tu_annotate.Rmd		tu_annotate.Rmd

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