From e4e2b7c9b8728ad3c53c8619af9bcbb6a5ace39f Mon Sep 17 00:00:00 2001 From: coolneng Date: Tue, 4 May 2021 11:12:47 +0200 Subject: [PATCH] Remove redundant directories --- data/reports/.gitkeep | 0 docs/notebook.org | 46 ------------------------------------------- 2 files changed, 46 deletions(-) delete mode 100644 data/reports/.gitkeep delete mode 100644 docs/notebook.org diff --git a/data/reports/.gitkeep b/data/reports/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/docs/notebook.org b/docs/notebook.org deleted file mode 100644 index 5b8a08e..0000000 --- a/docs/notebook.org +++ /dev/null @@ -1,46 +0,0 @@ -#+TITLE: locigenesis -#+AUTHOR: Amin Kasrou Aouam -#+DATE: 2021-03-10 -* Sequence alignment - -Our generated sequences contain the full VJ region, but we are only interested in the CDR3 (Complementarity-determining region). We will proceed by delimiting CDR3, using the known sequences of V and J. - -#+begin_src R :results value silent -v_segments <- readRDS("data/v_segments.rds") -j_segments <- readRDS("data/j_segments_phe.rds") -#+end_src - -#+begin_src R -print(v_segments) -print(j_segments) -#+end_src - -#+RESULTS: -#+begin_example - A DNAStringSet instance of length 147 - width seq names - [1] 326 GATACTGGAATTACCCAGACAC...ATCTCTGCACCAGCAGCCAAGA TRBV1*01_P - [2] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*01_F - [3] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*02_F - [4] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*01_F - [5] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*02_F - ... ... ... -[143] 324 GATACTGGAGTCTCCCAGAACC...GTATCTCTGTGCCAGCACGTTG TRBV7-9*06_(F) -[144] 323 .........................TGTATCTCTGTGCCAGCAGCAG TRBV7-9*07_(F) -[145] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*01_F -[146] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*02_F -[147] 321 GATTCTGGAGTCACACAAACCC...TTTGTATTTCTGTGCCAGCAGC TRBV9*03_(F) - A DNAStringSet instance of length 16 - width seq names - [1] 32 TGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG TRBJ2-2P*01_ORF - [2] 31 TTTGGAGAGGGAAGTTGGCTCACTGTTGTAG TRBJ1-3*01_F - [3] 31 TTTGGTGATGGGACTCGACTCTCCATCCTAG TRBJ1-5*01_F - [4] 31 TTTGGCAGTGGAACCCAGCTCTCTGTCTTGG TRBJ1-4*01_F - [5] 31 TTCGGTTCGGGGACCAGGTTAACCGTTGTAG TRBJ1-2*01_F - ... ... ... -[12] 31 TTTGGCCCAGGCACCCGGCTGACAGTGCTCG TRBJ2-3*01_F -[13] 31 TTCGGGCCAGGCACGCGGCTCCTGGTGCTCG TRBJ2-5*01_F -[14] 31 TTCGGGCCAGGGACACGGCTCACCGTGCTAG TRBJ2-1*01_F -[15] 31 TTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*01_F -[16] 31 GTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*02_ORF -#+end_example