berman-lab ymap issues - Githubissues

berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.

MIT License

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issues

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Current version updates

#71 darrenabbey closed 1 year ago
0
update

#70 darrenabbey closed 1 year ago
0
Exploit fix

#69 darrenabbey closed 1 year ago
0
Uploading .fna references fails

#68 vladimirg opened 2 years ago
0
ddRADseq analysis output missing the SNP BED track

#67 vladimirg closed 7 years ago
1
FastQC quality extraction step fails when datafiles end with .fq

#66 vladimirg opened 7 years ago
0
Parental strain combo box shows many blanks

#65 vladimirg opened 7 years ago
1
When uploading a BAM file, it's not deleted in the cleanup script

#64 vladimirg closed 7 years ago
0
FASTQC current version change

#63 darrenabbey closed 7 years ago
4
Input file names aren't adequately sanitized.

#62 darrenabbey opened 7 years ago
0
Input file processing errors not displayed.

#61 darrenabbey opened 7 years ago
0
FASTA index creation error

#60 darrenabbey closed 7 years ago
2
Genome install extra step / repetitiveness plot figure?

#59 darrenabbey opened 7 years ago
7
Large reference genomes (>100 Mbps) crash both at the reference upload and the dataset analysis stages

#58 vladimirg closed 7 years ago
3
Location of segments doesn't display good in matlab 2016a

#57 ghost closed 7 years ago
1
Wrong segmentation in ChARM

#56 ghost closed 7 years ago
1
Allow users to download a zipped bundle of analysis results per dataset

#55 vladimirg opened 7 years ago
0
Monitor dataset analysis for errors and save input files for a post-mortem

#54 vladimirg opened 7 years ago
0
Incorrect cutoff detection in allele ratios

#53 vladimirg opened 7 years ago
8
Auto-detection of baseline ploidy

#52 vladimirg opened 7 years ago
5
Standard presentation in datasets with a parental strain can be confusing

#51 vladimirg opened 7 years ago
0
Creating fire plot takes too much time

#50 ghost closed 7 years ago
4
Possible error in SNP coloring

#49 ghost closed 7 years ago
3
Wrong read of CNV

#48 ghost closed 7 years ago
1
Combining figures doesn't work in Matlab 2014

#47 vladimirg closed 7 years ago
1
Combining figures with new datasets requires pressing the combine button again

#46 vladimirg closed 7 years ago
1
Consider using pipes instead of writing to disk

#45 vladimirg opened 7 years ago
0
Write out stderr of all tools to a log

#44 vladimirg opened 8 years ago
0
Uploading datasets is fragile

#43 vladimirg opened 8 years ago
0
Single end ddRADseq crashes

#42 vladimirg closed 7 years ago
0
Aberrent SNP ratios in homozygous regions.

#41 darrenabbey opened 8 years ago
2
Implement a quota system

#40 vladimirg closed 7 years ago
3
Chromosomes that don't have any reads mapping to them can crash the analysis

#39 vladimirg closed 7 years ago
0
Visualization too crowded for too many chromosomes

#38 vladimirg closed 7 years ago
4
Logging to integration site causes login to production site

#37 ghost opened 8 years ago
0
Upgrade samtools to allow parallelization

#36 vladimirg closed 8 years ago
1
Add 'debug mode' flag to keep intermediary files

#35 vladimirg closed 8 years ago
0
Whole-genome analysis crashes when chromosomes in reference genome are too short

#34 vladimirg closed 7 years ago
3
"Fat" CNV bars in lovelace

#33 vladimirg closed 7 years ago
5
Add parallelization to the configuration

#32 vladimirg closed 8 years ago
1
Junk errors in Apache log

#31 ghost opened 8 years ago
0
Multiple session starts

#30 ghost opened 8 years ago
0
Redundant POST/GET variables

#29 ghost closed 8 years ago
1
Remove FTP drop

#28 ghost closed 8 years ago
1
Adding new genome does not display well

#27 ghost opened 8 years ago
0
Logon error message dissapears

#26 ghost opened 8 years ago
2
Permissions for files on the webserver

#25 vladimirg opened 8 years ago
1
The string 'fastq' in project names breaks analysis

#24 vladimirg closed 8 years ago
1
Running ddRADseq without fragment-length bias correction gives errors

#23 vladimirg closed 7 years ago
5
Remove FTP drop from UI

#22 vladimirg closed 8 years ago
1