Commit 918b8907 authored by Thomas Schwarzl's avatar Thomas Schwarzl
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parent 74cc60e6
......@@ -2,3 +2,5 @@
.Rhistory
.RData
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sizes.pdf
---
title: "2CRICAnalysis"
title: "2C-RIC Analysis"
author: "Thomas Schwarzl"
output: html_document
---
2C RIC Analysis
There are two 2C-RIC runs. The first one with
is RBPBASE000000056.1 Sc_Asencio-2C Sc_2C-TRIC
......@@ -597,6 +595,14 @@ RA$save_venn(selection_ids = c(TRIC, any2C_run2, RA$get_anyRIC_id()),
```
```{r}
RA$save_venn(selection_ids = c(any2C_id, TRAPP_id, RA$get_anyRIC_id()),
names = c("any 2C", "TRAP", "any Sc, Mm, Hs"),
file_root = file.path(output_dir, "2C_TRAP_ScMmHs_venn"),
fill = cbbPalette[c(6,7,3)])
```
```{r}
RA$save_venn(selection_ids = c(TRIC, TRIC_2, sTRIC_2),
names = c("2C TRIC(1)", "2C TRIC(2)", "2C RIC(2)"),
......
Pab1_input_rep1__1 rawnodup 12705319
Pab1_input_rep1__1 raw 15450803
Pab1_input_rep1__2 rawnodup 12705319
Pab1_input_rep1__2 raw 15450803
Pab1_input_rep2__1 rawnodup 10468318
Pab1_input_rep2__1 raw 12308885
Pab1_input_rep2__2 rawnodup 10468318
Pab1_input_rep2__2 raw 12308885
Pab1_input_rep3__1 rawnodup 10292675
Pab1_input_rep3__1 raw 12010593
Pab1_input_rep3__2 rawnodup 10292675
Pab1_input_rep3__2 raw 12010593
Pab1_IP_rep1__1 rawnodup 11820622
Pab1_IP_rep1__1 raw 19841436
Pab1_IP_rep1__2 rawnodup 11820622
Pab1_IP_rep1__2 raw 19841436
Pab1_IP_rep2__1 rawnodup 15667957
Pab1_IP_rep2__1 raw 21725307
Pab1_IP_rep2__2 rawnodup 15667957
Pab1_IP_rep2__2 raw 21725307
Pab1_IP_rep3__1 rawnodup 11035166
Pab1_IP_rep3__1 raw 20040366
Pab1_IP_rep3__2 rawnodup 11035166
Pab1_IP_rep3__2 raw 20040366
T3_IP_rep1_ProtA_1 rawnodup 16037696
T3_IP_rep1_ProtA_1 raw 23194967
T3_IP_rep1_ProtA_2 rawnodup 16037696
T3_IP_rep1_ProtA_2 raw 23194967
T3_IP_rep2_ProtA_1 rawnodup 17117513
T3_IP_rep2_ProtA_1 raw 25695644
T3_IP_rep2_ProtA_2 rawnodup 17117513
T3_IP_rep2_ProtA_2 raw 25695644
T3_IP_rep3_ProtA_1 rawnodup 23889806
T3_IP_rep3_ProtA_1 raw 40914534
T3_IP_rep3_ProtA_2 rawnodup 23889806
T3_IP_rep3_ProtA_2 raw 40914534
T3_input_rep1_TAP_1 rawnodup 7086445
T3_input_rep1_TAP_1 raw 8173638
T3_input_rep1_TAP_2 rawnodup 7086445
T3_input_rep1_TAP_2 raw 8173638
T3_input_rep2_TAP_1 rawnodup 14803506
T3_input_rep2_TAP_1 raw 17986397
T3_input_rep2_TAP_2 rawnodup 14803506
T3_input_rep2_TAP_2 raw 17986397
Pab1_input_rep1_noRiboDepletion_1 rawnodup 9343611
Pab1_input_rep1_noRiboDepletion_1 raw 10557154
Pab1_input_rep1_noRiboDepletion_2 rawnodup 9343611
Pab1_input_rep1_noRiboDepletion_2 raw 10557154
T3_input_rep3_TAP_1 rawnodup 13426538
T3_input_rep3_TAP_1 raw 15120629
T3_input_rep3_TAP_2 rawnodup 13426538
T3_input_rep3_TAP_2 raw 15120629
T3_IP_rep1_TAP_1 rawnodup 13089080
T3_IP_rep1_TAP_1 raw 19199068
T3_IP_rep1_TAP_2 rawnodup 13089080
T3_IP_rep1_TAP_2 raw 19199068
T3_IP_rep2_TAP_1 rawnodup 17932819
T3_IP_rep2_TAP_1 raw 25380589
T3_IP_rep2_TAP_2 rawnodup 17932819
T3_IP_rep2_TAP_2 raw 25380589
T3_IP_rep3_TAP_1 rawnodup 10959562
T3_IP_rep3_TAP_1 raw 17456416
T3_IP_rep3_TAP_2 rawnodup 10959562
T3_IP_rep3_TAP_2 raw 17456416
WT_input_rep1__1 rawnodup 11679517
WT_input_rep1__1 raw 13640348
WT_input_rep1__2 rawnodup 11679517
WT_input_rep1__2 raw 13640348
WT_input_rep2__1 rawnodup 12133296
WT_input_rep2__1 raw 14044800
WT_input_rep2__2 rawnodup 12133296
WT_input_rep2__2 raw 14044800
WT_input_rep3__1 rawnodup 13042521
WT_input_rep3__1 raw 15507636
WT_input_rep3__2 rawnodup 13042521
WT_input_rep3__2 raw 15507636
WT_IP_rep1__1 rawnodup 4785341
WT_IP_rep1__1 raw 10048705
WT_IP_rep1__2 rawnodup 4785341
WT_IP_rep1__2 raw 10048705
WT_IP_rep2__1 rawnodup 15133143
WT_IP_rep2__1 raw 24085039
WT_IP_rep2__2 rawnodup 15133143
WT_IP_rep2__2 raw 24085039
WT_IP_rep3__1 rawnodup 4248838
WT_IP_rep3__1 raw 9606326
WT_IP_rep3__2 rawnodup 4248838
WT_IP_rep3__2 raw 9606326
Pab1_input_rep2_noRiboDepletion_1 rawnodup 8276919
Pab1_input_rep2_noRiboDepletion_1 raw 9287506
Pab1_input_rep2_noRiboDepletion_2 rawnodup 8276919
Pab1_input_rep2_noRiboDepletion_2 raw 9287506
Pab1_input_rep3_noRiboDepletion_1 rawnodup 9400677
Pab1_input_rep3_noRiboDepletion_1 raw 10560741
Pab1_input_rep3_noRiboDepletion_2 rawnodup 9400677
Pab1_input_rep3_noRiboDepletion_2 raw 10560741
T3_input_rep1_ProtA_1 rawnodup 11607489
T3_input_rep1_ProtA_1 raw 13714323
T3_input_rep1_ProtA_2 rawnodup 11607489
T3_input_rep1_ProtA_2 raw 13714323
T3_input_rep2_ProtA_1 rawnodup 12786482
T3_input_rep2_ProtA_1 raw 15621927
T3_input_rep2_ProtA_2 rawnodup 12786482
T3_input_rep2_ProtA_2 raw 15621927
T3_input_rep3_ProtA_1 rawnodup 10705471
T3_input_rep3_ProtA_1 raw 12261361
T3_input_rep3_ProtA_2 rawnodup 10705471
T3_input_rep3_ProtA_2 raw 12261361
Gene stable ID Gene name Gene description
Q0158 21S_RRNA Mitochondrial 21S rRNA; intron encodes the I-SceI DNA endonuclease [Source:SGD;Acc:S000007288]
RDN58-2 RDN58-2 5.8S ribosomal RNA (5.8S rRNA); component of the large (60S) ribosomal subunit; encoded in the rDNA repeat (RDN1) [Source:SGD;Acc:S000006489]
RDN5-1 RDN5-1 5S ribosomal RNA (5S rRNA); only complete sequence of 6 repeated RDN5 alleles; able to support viability when provided as sole form of 5S rRNA; component of the large (60S) ribosomal subunit; localized to the nucleolus via interaction with Rpl5p; may play a role in translational frame fidelity; transcription is mediated by PolIII and activated by TFIIIA and TFIIIE [Source:SGD;Acc:S000006479]
RDN5-6 RDN5-6 Variant 5S ribosomal rRNA (5S rRNA) gene; located at a site distal to the RDN1 locus [Source:SGD;Acc:S000029711]
RDN37-2 RDN37-2 35S ribosomal RNA (35S rRNA) transcript; encoded by the RDN1 locus; processed into the 25S, 18S and 5.8S rRNAs (represented by the RDN25, RDN18, and RDN58 loci) [Source:SGD;Acc:S000006487]
RDN5-3 RDN5-3 Variant 5S ribosomal RNA (5S rRNA) gene; located at a site distal to the RDN1 locus; unable to support cell viability when provided as sole source of 5S rRNA; identical in sequence to variant alleles RDN5-2, RDN5-4, and RDN5-5 [Source:SGD;Acc:S000006481]
ITS1-2 Non-coding region between RDN58 and RDN18; transcribed as part of the 35S rRNA precursor transcript; excision during transcript maturation is coupled with processing of the 3' external transcribed spacer (3' ETS) [Source:SGD;Acc:S000029709]
ETS1-2 Non-coding region located immediately upstream of RDN18; transcribed as part of the 35S rRNA precursor transcript; contains an essential U3 snoRNA binding site required for maturation of 18S rRNA [Source:SGD;Acc:S000029707]
RDN37-1 RDN37-1 35S ribosomal RNA (35S rRNA) transcript; encoded by the RDN1 locus; processed into the 25S, 18S and 5.8S rRNAs (represented by the RDN25, RDN18, and RDN58 loci) [Source:SGD;Acc:S000006486]
ITS1-1 Non-coding region between RDN58 and RDN18; transcribed as part of the 35S rRNA precursor transcript; excision during transcript maturation is coupled with processing of the 3' external transcribed spacer (3'ETS) [Source:SGD;Acc:S000029715]
RDN5-4 RDN5-4 Variant 5S ribosomal rRNA (5S rRNA) gene; located at a site distal to the RDN1 locus; unable to support cell viability when provided as sole source of 5S rRNA; identical in sequence to variant alleles RDN5-2, RDN5-3, and RDN5-5 [Source:SGD;Acc:S000029708]
RDN25-1 RDN25-1 25S ribosomal RNA (25S rRNA); component of the large (60S) ribosomal subunit; encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript; formed by endonucleolytic cleavage at the C2 site of internal transcribed spacer 2 (ITS2) [Source:SGD;Acc:S000006484]
ETS2-1 Non-coding region located adjacent to and downstream of RDN25; transcribed as part of the 35S rRNA precursor transcript; contains the primary rRNA transcription termination site at +93 and a secondary termination site between +211 and +250 [Source:SGD;Acc:S000029718]
RDN58-1 RDN58-1 5.8S ribosomal RNA (5.8S rRNA); component of the large (60S) ribosomal subunit; encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript; 3' end formation involves processing by the exosome complex while 5' end is generated by Kem1p and Rat1p [Source:SGD;Acc:S000006488]
RDN25-2 RDN25-2 25S ribosomal RNA (25S rRNA); component of the large (60S) ribosomal subunit; encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript; formed by endonucleolytic cleavage at the C2 site of internal transcribed spacer 2 (ITS2) [Source:SGD;Acc:S000006485]
RDN18-2 RDN18-2 18S ribosomal RNA (18S rRNA); component of the small (40S) ribosomal subunit; involved in codon recognition by tRNAs or the release factor eRF1 (Sup45p); encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript [Source:SGD;Acc:S000006483]
RDN5-2 RDN5-2 Variant 5S ribosomal rRNA (5S rRNA) gene; located within the RDN1 locus; unable to support cell viability when provided as sole source of 5S rRNA; identical in sequence to variant alleles RDN5-3, RDN5-4, and RDN5-5 [Source:SGD;Acc:S000006480]
ETS1-1 Non-coding region located immediately upstream of RDN18; transcribed as part of the 35S rRNA precursor transcript; contains an essential U3 snoRNA binding site required for maturation of 18S rRNA [Source:SGD;Acc:S000029717]
ITS2-1 Non-coding region between RDN58 and RDN25; transcribed as part of the 35S rRNA precursor transcript; forms a stem-loop structure that is required for processing of the precursor transcript [Source:SGD;Acc:S000029716]
RDN5-5 RDN5-5 Variant 5S ribosomal rRNA (5S rRNA) gene; located at a site distal to the RDN1 locus; unable to support cell viability when provided as sole source of 5S rRNA; identical in sequence to variant alleles RDN5-2, RDN5-3, and RDN5-4 [Source:SGD;Acc:S000029710]
Q0020 15S_RRNA Ribosomal RNA of the small mitochondrial ribosomal subunit; MSU1 allele suppresses ochre stop mutations in mitochondrial protein-coding genes [Source:SGD;Acc:S000007287]
RDN18-1 RDN18-1 18S ribosomal RNA (18S rRNA); component of the small (40S) ribosomal subunit; involved in codon recognition by tRNAs or the release factor eRF1 (Sup45p); encoded in the rDNA repeat (RDN1) as part of the 35S primary transcript [Source:SGD;Acc:S000006482]
ITS2-2 Non-coding region between RDN58 and RDN25; transcribed as part of the 35S rRNA precursor transcript; forms a stem-loop structure required for processing of the precursor transcript [Source:SGD;Acc:S000029712]
ETS2-2 Non-coding region located adjacent to RDN25; transcribed as part of the 35S rRNA precursor transcript; contains the primary rRNA transcription termination site at +93 and a secondary termination site between +211 and +250 [Source:SGD;Acc:S000029713]
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