heathsc gemBS issues - Githubissues

heathsc / gemBS

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

GNU General Public License v3.0

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methylation and SNP difference

#103 TheRainInSpain opened 3 months ago
0
documentation page not find

#102 TheRainInSpain opened 4 months ago
1
Documentation (with SSL) cannot be accessed

#101 IsmailM opened 8 months ago
0
mapped bam files: SM key without value

#100 NikolausMandlburgerCCRI opened 1 year ago
0
bs_call finished with -6

#99 PrashantKuntala opened 1 year ago
0
snp extract "Invalid format"

#98 xiaoqiwang19 opened 1 year ago
4
System.Error::Signal raised (no=11) using bs_call

#97 dy-lin opened 1 year ago
2
Difference between bin/bs_call and gemBSbinaries/bs_call?

#96 dy-lin opened 1 year ago
3
The .bed file does not match the statistics of the REPORT

#95 ReinaWei opened 1 year ago
0
mapping merge fails if one of the file_id's is equal to the Barcode

#94 IsmailM opened 2 years ago
0
HowTo enable GPU for read mapping?

#93 claus-h-g opened 2 years ago
7
Error when running gemBS map

#92 boconnell89 closed 2 years ago
3
Alignment Modes

#91 HarryZhang1224 closed 2 years ago
9
ValueError: Error while executing the Bisulfite bisulphite-mapping

#90 paul-sud opened 2 years ago
14
The upside down

#89 JakeLehle closed 2 years ago
0
gemBS 3.5.1 issue at map stage of sample data

#88 JakeLehle closed 2 years ago
10
Dealing with overlapping reads

#87 IsmailM closed 2 years ago
3
Latest version to Bioconda?

#86 ebprideaux closed 2 years ago
9
Conversion rate is N/A in QC

#85 paul-sud closed 2 years ago
7
Scattering gemBS alignment step across a cluster

#84 gilhornung opened 3 years ago
1
Can't see colors for ENCODE bigBed on UCSC browser

#83 paul-sud opened 3 years ago
4
PBAT dataset failed in calling step

#82 ifishlin opened 3 years ago
3
how to set the control sequences?

#81 biozzq opened 3 years ago
0
Logging error on call

#80 wynstep closed 3 years ago
2
methylation calling issue on cluster

#79 wynstep opened 3 years ago
1
Cannot install gemBS

#78 wynstep closed 3 years ago
3
R1 and R2 specific left and right trim values

#77 will-NYGC closed 3 years ago
4
SNP extraction

#76 IsmailM opened 4 years ago
2
Wrong coverage

#75 wynstep opened 4 years ago
3
Installation error (min gcc version required )

#74 IsmailM closed 4 years ago
4
gemBS index failure: bgzip not found

#73 paul-sud closed 4 years ago
3
Specify target regions for snp calling && Extract SNPs only within target regions

#72 AndyWangSFU opened 4 years ago
10
package/dependencies calling errors || "too many values to unpack"

#71 AndyWangSFU closed 4 years ago
6
wigToBigWig error during extract

#70 paul-sud closed 4 years ago
3
gemBS extract bed file has incorrect delimiters

#69 paul-sud closed 4 years ago
6
gemBS prepare

#68 edsu7 closed 4 years ago
4
analyze methyl-capture data

#67 RichardCorbett opened 4 years ago
0
error "unrecognized CIGAR operator" when run gemBS map

#66 fyymxb opened 4 years ago
1
error in gembs index

#65 sitag closed 4 years ago
4
Reference file 'path/to/file' does not exist

#64 paulstretenowich closed 4 years ago
4
error during "extract" with container - possibly bcftools plugins related

#63 RichardCorbett closed 4 years ago
14
Documentation offline

#62 IsmailM opened 4 years ago
0
gemBS index fails at 50%

#61 paul-sud closed 5 years ago
3
Conversion rates are missing for some of the samples

#60 berguner opened 5 years ago
3
Error using gemBS extract - a reference genome problem?

#59 DolapoA closed 5 years ago
1
error running gemBS call

#58 lrsantiago opened 5 years ago
9
Mapping with singularity gemBS

#57 DolapoA closed 5 years ago
2
Typo

#56 kgurushankar opened 5 years ago
0
Attribute error

#55 kkleinoros closed 4 years ago
10
Slowness when running

#54 paulstretenowich opened 5 years ago
2