chasewnelson SNPGenie issues

chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

GNU General Public License v3.0

100 stars 37 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

problem with minfreq

#74 wantingwei opened 4 months ago
5
Warning for coverage and nucleotide sums

#73 shamavirani closed 6 months ago
3
Issue with SNPGenie_sliding_windows.R

#72 OmonkeyGOD closed 10 months ago
4
No snps problems

#71 NiklausMikaelson12138 opened 12 months ago
4
VCF has no header

#70 NiklausMikaelson12138 opened 1 year ago
0
gtf2revcom.pl script issue

#69 georgysemenov closed 1 year ago
2
Using SNPGenie on VCF from RAD-seq

#68 AudeCaizergues opened 1 year ago
1
CDS annotation(s) does not have a gene_id

#67 frith6 closed 1 year ago
2
Need help to determine method for inference of convergent evolution

#66 qianxuans opened 1 year ago
1
GTF file does not contain any sense (+) strand products

#65 dferran1 opened 1 year ago
12
How to join the output for a whole genome analysis

#64 pabloangulo7 opened 1 year ago
5
All classified as synonymous

#63 marotbone closed 1 year ago
3
within-host diversity analysis : one individual, different time-points

#62 PegahDan closed 1 year ago
4
within-host diversity influenza whole genome

#61 Su06690 closed 1 year ago
11
Coverage warning

#60 dinahparker closed 2 years ago
4
SNP genie

#59 Ravy-LFL opened 2 years ago
0
Empty output

#58 White-Shinobi closed 2 years ago
8
What is the best option?

#57 glaudelrio opened 2 years ago
1
Negative values for mean_gdiv_polymorphic

#56 peterdfields opened 2 years ago
1
triplet error for spliced proteins

#55 hrrsjeong opened 2 years ago
2
unsure how SNPgenie does the polarization of mutations

#54 mufernando opened 2 years ago
1
Sliding window analysis for the spliced protein

#53 Chongli-90 closed 1 year ago
5
sliding_window script requires different headers than between_group output file generates

#52 passdan opened 3 years ago
4
NONREF_NONPOLY and population_summary.txt empty

#51 nicolo-tellini opened 3 years ago
2
pi cluster within-pool

#50 aspitaleri opened 3 years ago
11
Question on interpreting the output parameters

#49 Chongli-90 closed 1 year ago
5
Question about calculating pi within a window

#48 deborahmleigh opened 3 years ago
21
Watterson's theta and Tajima's D estimates

#47 sqiu86 closed 2 years ago
9
comments on dN/dS and pi

#46 aspitaleri closed 3 years ago
1
gtf -strand convert to + strand

#45 zlc289 opened 3 years ago
2
analysing within-host diversity

#44 aspitaleri opened 3 years ago
12
SNPGenie for bacterial samples from the same lineage

#43 arredondo23 closed 3 years ago
6
WARNING: AD must list numbers

#42 ireneIta opened 3 years ago
6
mid-sequence STOP codon in the sequence

#41 jsan4christ opened 3 years ago
1
SNPgenie for one bacterial strain

#40 SolayMane opened 3 years ago
1
Advice on multi-sample, multi-species, multi-contig analyses for both πN/πS and dN/dS

#39 andreaswallberg opened 3 years ago
4
specify genetic code?

#38 nathanerank opened 3 years ago
3
snpgenie\_within\_group.pl: Question about input file formats

#37 annasimonsen opened 3 years ago
2
error in running the SNPGenie

#36 shiyi-pan opened 3 years ago
16
How to properly format VCF for snpgenie.pl (when using VCFs from multiple isolates of a population)

#35 maxgmarin closed 3 years ago
7
between pops with vcf?

#34 karenbobier closed 3 years ago
3
Making a vcf file by hand: ## WARNING: ## The SNP Report table_1.csv has no header.

#33 padpadpadpad closed 3 years ago
3
Ignore genes that are not multiples of 3

#32 jckhearn opened 4 years ago
2
Tag a release?

#31 druvus closed 4 years ago
2
Fix shebang

#30 druvus closed 4 years ago
0
reverse compliment

#29 harpur closed 4 years ago
6
Understanding how within-between group works.

#28 migrau closed 4 years ago
3
Missing sites in FASTA files

#27 sialsaffar closed 4 years ago
3
Hello, I am trying to run snpgenie_wthin_group.pl after installing Parallel::ForkManager (with -force option) and get the error message: MacBookPro:SNPGenie-master julia$ perl snpgenie_within_group.pl --fasta_file_name=compl_cons_ORF --gtf_file_name=GGS.gtf Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2/darwin-thread-multi-2level /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at snpgenie_within_group.pl line 62. BEGIN failed--compilation aborted at snpgenie_within_group.pl line 62. Do you have any idea what I can do to fix it? Thanks!!!

#26 jhillung closed 4 years ago
3
Batch processing

#25 mhopken closed 4 years ago
8