Move notebooks around

saketkc · Sep 26, 2018 · c10e2c4 · c10e2c4
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diff --git a/.gitignore b/.gitignore
diff --git a/GTF.py b/GTF.py
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/create_regions_from_gencode.R b/create_regions_from_gencode.R
diff --git a/create_without_rRNA_tRNA.sh b/create_without_rRNA_tRNA.sh
diff --git a/..._albicans_SC5314/A22_r50/C_albicans_SC5314_version_A22-s07-m01-r50_features.encode.gtf.gz b/..._albicans_SC5314/A22_r50/C_albicans_SC5314_version_A22-s07-m01-r50_features.encode.gtf.gz
diff --git a/data/C_albicans_SC5314/A22_r50/UTR3.bed.gz b/data/C_albicans_SC5314/A22_r50/UTR3.bed.gz
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diff --git a/data/GRCm38/vM11/transcripts.bed.gz b/data/GRCm38/vM11/transcripts.bed.gz
diff --git a/data/GRCm38/vM11/tx2gene.bed.gz b/data/GRCm38/vM11/tx2gene.bed.gz
diff --git a/data/GRCm38/vM14/3UTRs.bed.gz b/data/GRCm38/vM14/3UTRs.bed.gz
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diff --git a/data/GRCm38/vM14/cds.bed.gz b/data/GRCm38/vM14/cds.bed.gz
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diff --git a/data/GRCm38/vM14/tx2gene.bed.gz b/data/GRCm38/vM14/tx2gene.bed.gz
diff --git a/data/GRCz10/v91/UTR3.bed.gz b/data/GRCz10/v91/UTR3.bed.gz
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diff --git a/data/GRCz10/v91/tss_sites.bed.gz b/data/GRCz10/v91/tss_sites.bed.gz
diff --git a/extract_lincRNA.py b/extract_lincRNA.py
diff --git a/extract_rRNA.py b/extract_rRNA.py
diff --git a/extract_tRNA.py b/extract_tRNA.py
diff --git a/genepred_to_bed.py b/genepred_to_bed.py
diff --git a/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.UTR3.bed b/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.UTR3.bed
diff --git a/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.UTR5.bed b/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.UTR5.bed
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diff --git a/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.genes.bed b/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.genes.bed
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diff --git a/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.promoter.1000.bed b/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.promoter.1000.bed
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diff --git a/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.tRNA_sites.bed b/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.tRNA_sites.bed
diff --git a/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.tss_sites.bed b/gffutils_beds/GRCh38/v25/gencode.v25.gffutils.tss_sites.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.UTR3.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.UTR3.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.UTR5.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.UTR5.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.cds.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.cds.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.cds.left.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.cds.left.bed
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diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.exon.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.exon.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.genes.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.genes.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.intron.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.intron.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.polyA_sites.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.polyA_sites.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.promoter.1000.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.promoter.1000.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.start_codon.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.start_codon.bed
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diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.tRNA_sites.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.tRNA_sites.bed
diff --git a/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.tss_sites.bed b/gffutils_beds/GRCm38/vM11/gencode.vM11.gffutils.tss_sites.bed
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diff --git a/notebooks/MG1655.ipynb b/notebooks/MG1655.ipynb
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diff --git a/notebooks/Gffutils C_albicans-A22-r50.ipynb → ...archive/Gffutils C_albicans-A22-r50.ipynb b/notebooks/Gffutils C_albicans-A22-r50.ipynb → ...archive/Gffutils C_albicans-A22-r50.ipynb
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diff --git a/notebooks/mm10.ipynb b/notebooks/mm10.ipynb
diff --git a/notebooks/sacCerR64.ipynb b/notebooks/sacCerR64.ipynb
diff --git a/plot_size_distribution.py b/plot_size_distribution.py