README.md

In ginnyintifa/SeqQuery:

1. Installation

SeqQuery can be downloaded and installed in R as follows. As a prerequisite, devtools must be installed:

```{r, eval = F} install.packages("devtools")

Next, install `SeqQuery`:

```{r, eval = F}

library("devtools")
devtools::install_github("ginnyintifa/SeqQuery")
library(SeqQuery)

2. Function

Query a location/region on a chromosome.

Function seq_query takes the chromosome and the location range of interest as input parameters. It will return the nucleotide sequence as the first output. If the region of interest happens to be with in CDS (coding DNA sequence), the function will return the amino acids coded by the nucleotides and some other sequence information.

3. Input files

SeqQuery provided feature files

Several files need to be downloaded from the following WEBSITE before running SeqQuery:

• 1 mRNA codon book in codon_dictionary.Rds.

• 2 Processed GTF file for information on all the CDS in tgf_df_CDS.Rds.

• 3 DNA sequences of 24 chromosomes in the folder chormosomes, each file chr*_seq.Rds contains sequence for each chormosome.

The original GTF file and sequence fasta file are downloaded from GENCODE: https://www.gencodegenes.org/releases/current.html

4. Output

Output from seq_query is simple. First the nucleotide sequence will be printed. If the queried region happens to be in CDS, then the amino acids coded by the nucleotide sequence along with other transcription and translation information will be the return value of the function.

5. Example script

getit = seq_query(query_chr = "chr1",
                  query_pos_start = 1419546,
                  query_pos_end = 1419548,
                  proc_tgf_path = "/data/ginny/GENCODE",
                  proc_chr_path = "/data/ginny/GENCODE/chromosomes",
                  codon_dictionary_path = "/data/ginny/GENCODE")

getit                             

Output of the above calling:

Query nucleotide(s):  TGT 
Return transcription and translation information! 
> getit
   chr position_start position_end query_nucleotide query_codon query_codon_pos
1 chr1        1419546      1419548              TGT         GUC             0_2
2 chr1        1419546      1419548              TGT     AAU_GUC             3_2
3 chr1        1419546      1419548              TGT     AAU_GUC             3_2
4 chr1        1419546      1419548              TGT     AAU_GUC             3_2
5 chr1        1419546      1419548              TGT     AAU_GUC             3_2
  query_aa  source type start_position end_position score strand frame
1        V  HAVANA  CDS        1419545      1419549     .      -     2
2      N_V  HAVANA  CDS        1419237      1419549     .      -     1
3      N_V ENSEMBL  CDS        1419103      1419549     .      -     0
4      N_V  HAVANA  CDS        1419103      1419549     .      -     0
5      N_V  HAVANA  CDS        1419237      1419549     .      -     1
            gene_id     transcript_id      gene_type gene_name transcript_type
1 ENSG00000235098.8 ENST00000520296.5 protein_coding   ANKRD65  protein_coding
2 ENSG00000235098.8 ENST00000427211.3 protein_coding   ANKRD65  protein_coding
3 ENSG00000235098.8 ENST00000537107.5 protein_coding   ANKRD65  protein_coding
4 ENSG00000235098.8 ENST00000454272.2 protein_coding   ANKRD65  protein_coding
5 ENSG00000235098.8 ENST00000442470.1 protein_coding   ANKRD65  protein_coding
  transcript_name exon_number           exon_id level        protein_id
1     ANKRD65-204           3 ENSE00003617803.1     1 ENSP00000429035.1
2     ANKRD65-201           3 ENSE00003635074.1     2 ENSP00000428419.1
3     ANKRD65-205           4 ENSE00002229397.2     3 ENSP00000445688.1
4     ANKRD65-203           3 ENSE00001784050.1     2 ENSP00000482314.1
5     ANKRD65-202           2 ENSE00001641431.1     2 ENSP00000428201.1
  havana_gene    havana_transcript
1        CCDS          CCDS57963.1
2 CCDS57962.1 OTTHUMG00000002911.4
3        CCDS          CCDS55558.1
4        CCDS          CCDS55558.1
5        CCDS          CCDS57962.1

ginnyintifa/SeqQuery documentation built on May 18, 2019, 11:28 p.m.