pauline-ng SIFT4G_Create_Genomic_DB issues

pauline-ng / SIFT4G_Create_Genomic_DB

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.

GNU General Public License v3.0

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issues

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Making database for sugarcane ends without warning or error

#101 Windyxia11 opened 3 weeks ago
0
Pos with confident scores < 90%

#100 mmlian opened 3 weeks ago
0
No valid queries to process using bacterial gtf to build database

#99 dcarru01 opened 2 months ago
0
Making database for soybean ends without warning or error

#98 noobylf opened 3 months ago
0
Use of uninitialized value in concatenation (.) or string at make-single-records-BIOPERL.pl line 305.

#97 NicMAlexandre opened 3 months ago
1
Creating local database is always interrupted at aligning step

#96 clavedec opened 5 months ago
3
Possible precedence issue with control flow operator at

#95 fan040 closed 5 months ago
0
MSG: Each line of the qual file must be less than 65,536 characters. Line 3 is 604927368 chars.

#94 fan040 closed 6 months ago
3
cat: '/cluster/home/fanrong/perl5/scripts_to_build_SIFT_db/test_files/AK58V4MP/fasta/*.fasta': 没有那个文件或目录

#93 fan040 closed 6 months ago
15
Reference genome

#92 liulu0827 opened 7 months ago
1
Problem with Creating Local Database

#91 VNF1981 closed 8 months ago
3
error no such file or directory

#90 sagitaninta closed 10 months ago
3
Add docker

#89 pauline-ng closed 1 year ago
0
chr naming

#88 pauline-ng closed 1 year ago
3
No error message but nothing in results file

#87 ksolari opened 1 year ago
11
Perl problem test data

#86 gubrins closed 1 year ago
21
The build database ran successfully but there was no results file

#85 abcdefghijklmn97 closed 1 year ago
15
Creating SIFT database from local genomic and gtf file with test data does not work

#84 gubrins closed 1 year ago
5
Making database for Culex Tarsalis ends without after processing queries with no warning or error

#83 Afei99357 opened 1 year ago
17
has error during create new database for Culex Tarsalis (invalid chain data)

#82 Afei99357 closed 1 year ago
2
Possible fasta related errors with creating a database

#81 hclendenin closed 1 year ago
17
* processing database part 1 (size ~0.25 GB): 100.00/100.00% *

#80 wanggshuoo closed 1 year ago
3
error in building database

#79 AmruthaJNC opened 1 year ago
19
Error in building database for new species

#78 rebecca-sh closed 1 year ago
9
Fixing the internal links in README.md

#77 MCorentin opened 1 year ago
0
I can not creat database

#76 NiklausMikaelson12138 closed 1 year ago
3
files with lowercase nucleotides

#75 romseg opened 1 year ago
0
The database was not created successfully by SIFT4G_Create_Genomic_DB

#74 danrans123 closed 1 year ago
20
SIFT4G annotator

#73 yaada100 closed 1 year ago
15
SIFT4G Annotator Standalone annotates only "NA" in VCF file

#72 mtejura closed 2 years ago
19
Feature request - sift4g --thread

#71 m3hdad closed 2 years ago
1
Errors in building my own database for rheMac10

#70 npb596 closed 1 year ago
39
Can not build my own SIFT database

#69 XIAO2Mark closed 2 years ago
14
Use of uninitialized value $fasta_subseq in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 446, <IN_TX> line 62209.

#68 thuynnguyen closed 2 years ago
15
For the annotation of Indel?

#67 yilunhuangyue closed 2 years ago
1
Using human test files: 'Pos with Confident Scores' is low in "CHECK_GENES.LOG"

#66 Melanie-Wilkinson closed 2 years ago
3
'Pos with Confident Scores' is low in "CHECK_GENES.LOG"

#65 wpf95 closed 2 years ago
2
Issue annotating VCF files with SIFT database

#64 frankiefattorini closed 2 years ago
11
building database

#63 pauline-ng closed 2 years ago
1
mitochondrial code

#62 pauline-ng closed 2 years ago
3
SIFT4G_Create_Genomic_DB

#61 PrincyJohnson closed 2 years ago
6
Issue making SIFT database from local genomic and gene annotation file (.gtf)

#60 frankiefattorini closed 2 years ago
5
Use of uninitialized value $fasta_subseq in concatenation (.) or string at generate-fasta-subst-files-BIOPERL.pl line 446, <IN_TX> line 37345.

#59 lizhiminlhy closed 2 years ago
1
processing database part 975 than finish，and nothing generate

#58 wpf95 closed 2 years ago
2
How to address poor database statistics

#57 andrewSharo closed 2 years ago
14
Questions regarding the results

#56 yaada100 closed 2 years ago
3
Questions regarding Query IDs construction

#55 yaada100 closed 2 years ago
3
Database creation – can’t open input files for new organism

#54 Melanie-Wilkinson closed 2 years ago
9
Errors while populating the databases; all files within singleRecords_with_scores folder removed

#53 Arynio closed 2 years ago
2
** Checking query data and substitutions files ** terminate called after throwing an instance of 'std::regex_error' what(): regex_error Aborted (core dumped)

#52 Jiangjiangzhang6 closed 2 years ago
1