jsh58 Genrich issues - Githubissues

jsh58 / Genrich

Detecting sites of genomic enrichment

MIT License

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Is this miss expected?

#62 dariober closed 3 years ago
3
Convert BedGraph-ish files to BedGraph files

#61 matwgmkw closed 3 years ago
1
Differences in Peaks

#60 genomebio-nk closed 3 years ago
3
Obtaining differential peaks with genrich replicate mode outputs

#59 jffchen closed 3 years ago
3
Appropriate area under the curve cut-off for ChIP-seq data

#58 HuynhNPT closed 4 years ago
2
Differential Peak Analysis

#57 liangcmu closed 4 years ago
3
Large difference in Peak number.

#56 Adnanhashim closed 4 years ago
2
Making sense of verbose output, especially re PCR duplicates

#55 levlitichev closed 4 years ago
2
Error! Experimental sample has no analyzable fragments

#54 ofirgriess closed 4 years ago
8
Mem limit error

#53 Ru194 closed 4 years ago
3
BAM5: poorly formatted SAM/BAM record

#52 GBeattie closed 4 years ago
2
Single-end ChIP-seq: difference between running replicates together or separately

#51 Simso86 closed 4 years ago
5
PCR duplicates detected from different Genrich runs

#50 elenichri closed 4 years ago
2
Citation

#49 radio1988 opened 4 years ago
0
Pre-marked duplicate read removal

#48 Maarten-vd-Sande closed 4 years ago
2
PCR duplicate removal

#47 elenichri closed 4 years ago
10
Error! Cannot parse BAM file

#46 ScientistJake closed 4 years ago
3
Peaks in different replicates

#45 sue02 closed 4 years ago
0
Peaks in different replicates

#44 sue02 closed 4 years ago
1
Question regarding ATAC-Seq replicates with varying readlengths

#43 malcook closed 4 years ago
1
Error! 'x': unknown value type in BAM auxiliary field

#42 alund1394 closed 4 years ago
1
`genrich -y` on single-end chip without replicates emits q-value of -1 across the board

#41 malcook closed 4 years ago
1
Feature Request: new option -i and -I to complement -e and -E

#40 malcook opened 4 years ago
6
Different pileups same(-ish) BAM

#39 Maarten-vd-Sande closed 4 years ago
2
How are summit p values calculated?

#38 AlexBlais74 closed 4 years ago
1
Follow Up: Genrich with reads from a tiny subset of genome #29

#37 vanottee closed 4 years ago
2
Genrich Publication

#36 elenichri closed 4 years ago
2
Question regarding read depth for control samples in ChiPseq

#35 linelieblein closed 4 years ago
1
Have you considered poisson distribution for q-value calculation?

#34 NyxSLY closed 4 years ago
2
More reads, less peaks

#33 daikisato12 closed 4 years ago
4
Input control DNA

#32 keenhl closed 4 years ago
1
Error! cannot open file for writing

#31 lindsaynhayes closed 4 years ago
4
Genrich for single-end ATAC-seq data

#30 amitjavilaventura closed 4 years ago
13
Genrich with reads from a tiny subset of genome

#29 AlexBlais74 closed 4 years ago
2
Genrich peak calls with and without control sample

#28 codingforwork closed 4 years ago
2
Periodicity of ATAC peak widths

#27 pgugger closed 4 years ago
5
Feature Request: Drop name-sort check

#26 ATpoint closed 4 years ago
4
Best peak-calling strategy for differential chromatin accessibility analysis: individual versus concatenated BAMs

#25 pgugger closed 4 years ago
3
Genrich for single-end ATAC-seq data

#24 ShuangHe33 closed 4 years ago
1
Expectations when excluding blacklist regions (-E)

#23 pgugger closed 4 years ago
10
ATAC-seq mode shifted the reads +4 bp for the +strand and -5 bp for the -strand

#22 ShuangHe33 closed 4 years ago
3
Conda buttons

#21 Maarten-vd-Sande closed 4 years ago
0
Conda package

#20 Maarten-vd-Sande closed 5 years ago
2
Unexpected replicate and compare outputs

#19 yhouvras closed 4 years ago
3
Segmentation fault: 11

#18 bigmonty12 closed 5 years ago
5
-V version not in help

#17 dariober closed 5 years ago
3
Segmentation fault

#16 JPascualAnaya closed 5 years ago
5
Genrich vs MACS2 or HMMRATTAC for ATAC-Seq

#15 jdidion closed 4 years ago
3
Peak detection when using multiple input BAM files

#14 ppnin closed 5 years ago
2
Multiple replicate files

#13 tcolston closed 5 years ago
2

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