Ecosyste.ms: Issues

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GitHub / jsh58/Genrich issues and pull requests

#105 - [Question]: Genrich ATAC-seq read-shifting peak calling

Issue - State: open - Opened by tamuanand over 1 year ago - 1 comment

#104 - Genrich output a broad peak file.

Issue - State: closed - Opened by justadustbuster over 1 year ago

#103 - HowTo call peaks from bigwig files?

Issue - State: open - Opened by malcook over 1 year ago - 1 comment

#101 - Removing PCR duplications gets more peaks ?

Issue - State: closed - Opened by akhst7 almost 2 years ago - 2 comments

#100 - link for awk command does not work

Issue - State: closed - Opened by ntsopoul almost 2 years ago - 1 comment

#99 - Can I use Genrich to call peaks from m6A (MeRIP)-seq data?

Issue - State: open - Opened by zhiyi1988 almost 2 years ago - 2 comments

#98 - program failed

Issue - State: closed - Opened by lmanchon about 2 years ago - 1 comment

#97 - Error! 635104 Cannot Convert to int

Issue - State: closed - Opened by tzvi909 about 2 years ago - 2 comments

#96 - Description of the -v option

Issue - State: closed - Opened by Le1223 over 2 years ago - 1 comment

#95 - Consider fragments file as input.

Issue - State: closed - Opened by maxim-h over 2 years ago - 2 comments

#94 - Number of peaks fall after including input DNA control

Issue - State: closed - Opened by keenhl over 2 years ago - 1 comment

#93 - Request optional fragment length filter

Issue - State: open - Opened by jmw86069 over 2 years ago - 2 comments

#92 - Genrich with Cut & Tag samples?

Issue - State: closed - Opened by r-mashoodh almost 3 years ago - 4 comments

#91 - Genrich with large number of samples

Issue - State: open - Opened by bwenz91 almost 3 years ago - 4 comments

#90 - Handle a subset of the reference genome during peak calling

Issue - State: closed - Opened by Simso86 almost 3 years ago - 1 comment

#89 - BedGraph-ish with replicates to BigWig

Issue - State: closed - Opened by Simso86 almost 3 years ago - 2 comments

#88 - on determining σ for p-value calculation

Issue - State: closed - Opened by malcook about 3 years ago - 4 comments

#87 - Peak summit

Issue - State: closed - Opened by wangxiangxiu about 3 years ago - 1 comment

#86 - Error! Cannot parse BAM file

Issue - State: closed - Opened by birkiy about 3 years ago - 1 comment

#85 - Genrich on bed derived bam file

Issue - State: open - Opened by emoiso about 3 years ago - 3 comments

#84 - About ATAC-seq peakcalling

Issue - State: closed - Opened by ChunjieJiang about 3 years ago - 2 comments

#83 - Background pileup value and AUC cutoff

Issue - State: closed - Opened by TeiturAK over 3 years ago - 1 comment

#82 - ATAC-seq pipeline

Issue - State: closed - Opened by LunaPatton over 3 years ago - 2 comments

#81 - "poorly formatted BED record" error on bed6 format

Issue - State: closed - Opened by lengie over 3 years ago - 2 comments

#80 - Peak calling missing closely located peaks?

Issue - State: open - Opened by Simso86 over 3 years ago - 4 comments

#79 - understanding origin of extremely broad peaks

Issue - State: closed - Opened by malcook over 3 years ago - 9 comments

#78 - peak calling with repeats

Issue - State: closed - Opened by 809825706 over 3 years ago - 3 comments

#77 - Discordant alignments and -y option in PE ATAC-Seq experiment

Issue - State: closed - Opened by uli-arb over 3 years ago - 1 comment

#76 - Error! Failure in ungetc() call

Issue - State: closed - Opened by shengxin321 over 3 years ago - 2 comments

#75 - Calculation of the p-value for a comprehensive calibration of minimum AUC

Issue - State: closed - Opened by lilian18100 over 3 years ago - 1 comment

#74 - Peak Calling with a Control or without

Issue - State: closed - Opened by lilian18100 almost 4 years ago - 1 comment

#73 - Calibration of the 'Minimum AUC for a peak' for Atac-seq

Issue - State: closed - Opened by lilian18100 almost 4 years ago - 4 comments

#72 - genrich fails with floating point error (136) on too much input

Issue - State: closed - Opened by malcook almost 4 years ago - 7 comments

#71 - bedgraphs normalization

Issue - State: closed - Opened by sunta3iouxos almost 4 years ago - 4 comments

#70 - Can not make

Issue - State: closed - Opened by GildasLepennetier about 4 years ago - 2 comments

#69 - bwa multimap reads

Issue - State: closed - Opened by sunta3iouxos about 4 years ago - 1 comment

#68 - Error code: "SAM/BAM file not sorted by queryname (samtools sort -n)"

Issue - State: closed - Opened by ydchung15 about 4 years ago - 2 comments

#67 - Update README.md

Pull Request - State: closed - Opened by malcook about 4 years ago - 1 comment

#66 - Allow Genrich to use reads marked as duplicate

Issue - State: closed - Opened by dariober about 4 years ago - 3 comments

#65 - Narrow and Broad Peaks

Issue - State: closed - Opened by Carmelo-Bravo about 4 years ago - 2 comments

#64 - More peaks in merged replicates than the sum of single replicates

Issue - State: closed - Opened by amitjavilaventura over 4 years ago - 1 comment

#63 - Minimum AUC settings for different number of reads

Issue - State: closed - Opened by ghost over 4 years ago - 1 comment

#62 - Is this miss expected?

Issue - State: closed - Opened by dariober over 4 years ago - 3 comments

#61 - Convert BedGraph-ish files to BedGraph files

Issue - State: closed - Opened by matwgmkw over 4 years ago - 1 comment

#60 - Differences in Peaks

Issue - State: closed - Opened by genomebio-nk over 4 years ago - 3 comments

#59 - Obtaining differential peaks with genrich replicate mode outputs

Issue - State: closed - Opened by jffchen over 4 years ago - 3 comments

#58 - Appropriate area under the curve cut-off for ChIP-seq data

Issue - State: closed - Opened by HuynhNPT over 4 years ago - 2 comments

#57 - Differential Peak Analysis

Issue - State: closed - Opened by liangcmu almost 5 years ago - 3 comments

#56 - Large difference in Peak number.

Issue - State: closed - Opened by Adnanhashim almost 5 years ago - 2 comments

#55 - Making sense of verbose output, especially re PCR duplicates

Issue - State: closed - Opened by levlitichev almost 5 years ago - 2 comments

#54 - Error! Experimental sample has no analyzable fragments

Issue - State: closed - Opened by ofirgriess almost 5 years ago - 8 comments

#53 - Mem limit error

Issue - State: closed - Opened by Ru194 almost 5 years ago - 3 comments

#52 - BAM5: poorly formatted SAM/BAM record

Issue - State: closed - Opened by GBeattie almost 5 years ago - 2 comments

#51 - Single-end ChIP-seq: difference between running replicates together or separately

Issue - State: closed - Opened by Simso86 almost 5 years ago - 5 comments

#50 - PCR duplicates detected from different Genrich runs

Issue - State: closed - Opened by elenichri almost 5 years ago - 2 comments

#49 - Citation

Issue - State: open - Opened by radio1988 almost 5 years ago

#48 - Pre-marked duplicate read removal

Issue - State: closed - Opened by Maarten-vd-Sande about 5 years ago - 2 comments

#47 - PCR duplicate removal

Issue - State: closed - Opened by elenichri about 5 years ago - 10 comments

#46 - Error! Cannot parse BAM file

Issue - State: closed - Opened by ScientistJake about 5 years ago - 3 comments

#45 - Peaks in different replicates

Issue - State: closed - Opened by sue02 about 5 years ago

#44 - Peaks in different replicates

Issue - State: closed - Opened by sue02 about 5 years ago - 1 comment

#43 - Question regarding ATAC-Seq replicates with varying readlengths

Issue - State: closed - Opened by malcook about 5 years ago - 1 comment

#42 - Error! 'x': unknown value type in BAM auxiliary field

Issue - State: closed - Opened by alund1394 about 5 years ago - 1 comment

#40 - Feature Request: new option -i and -I to complement -e and -E

Issue - State: open - Opened by malcook about 5 years ago - 6 comments

#39 - Different pileups same(-ish) BAM

Issue - State: closed - Opened by Maarten-vd-Sande over 5 years ago - 2 comments

#38 - How are summit p values calculated?

Issue - State: closed - Opened by AlexBlais74 over 5 years ago - 1 comment

#37 - Follow Up: Genrich with reads from a tiny subset of genome #29

Issue - State: closed - Opened by vanottee over 5 years ago - 2 comments

#36 - Genrich Publication

Issue - State: closed - Opened by elenichri over 5 years ago - 2 comments

#35 - Question regarding read depth for control samples in ChiPseq

Issue - State: closed - Opened by linelieblein over 5 years ago - 1 comment
Labels: good first issue

#34 - Have you considered poisson distribution for q-value calculation?

Issue - State: closed - Opened by NyxSLY over 5 years ago - 2 comments

#33 - More reads, less peaks

Issue - State: closed - Opened by daikisato12 over 5 years ago - 4 comments

#32 - Input control DNA

Issue - State: closed - Opened by keenhl over 5 years ago - 1 comment

#31 - Error! cannot open file for writing

Issue - State: closed - Opened by lindsaynhayes over 5 years ago - 4 comments

#30 - Genrich for single-end ATAC-seq data

Issue - State: closed - Opened by amitjavilaventura over 5 years ago - 13 comments

#29 - Genrich with reads from a tiny subset of genome

Issue - State: closed - Opened by AlexBlais74 over 5 years ago - 2 comments

#28 - Genrich peak calls with and without control sample

Issue - State: closed - Opened by codingforwork over 5 years ago - 2 comments

#27 - Periodicity of ATAC peak widths

Issue - State: closed - Opened by pgugger over 5 years ago - 5 comments

#26 - Feature Request: Drop name-sort check

Issue - State: closed - Opened by ATpoint over 5 years ago - 4 comments
Labels: enhancement

#24 - Genrich for single-end ATAC-seq data

Issue - State: closed - Opened by ShuangHe33 over 5 years ago - 1 comment

#23 - Expectations when excluding blacklist regions (-E)

Issue - State: closed - Opened by pgugger over 5 years ago - 10 comments

#22 - ATAC-seq mode shifted the reads +4 bp for the +strand and -5 bp for the -strand

Issue - State: closed - Opened by ShuangHe33 over 5 years ago - 3 comments

#21 - Conda buttons

Pull Request - State: closed - Opened by Maarten-vd-Sande over 5 years ago

#20 - Conda package

Issue - State: closed - Opened by Maarten-vd-Sande over 5 years ago - 2 comments

#19 - Unexpected replicate and compare outputs

Issue - State: closed - Opened by yhouvras over 5 years ago - 3 comments
Labels: good first issue

#18 - Segmentation fault: 11

Issue - State: closed - Opened by bigmonty12 over 5 years ago - 5 comments

#17 - -V version not in help

Issue - State: closed - Opened by dariober over 5 years ago - 3 comments

#16 - Segmentation fault

Issue - State: closed - Opened by JPascualAnaya over 5 years ago - 5 comments

#15 - Genrich vs MACS2 or HMMRATTAC for ATAC-Seq

Issue - State: closed - Opened by jdidion almost 6 years ago - 3 comments

#14 - Peak detection when using multiple input BAM files

Issue - State: closed - Opened by ppnin almost 6 years ago - 2 comments

#13 - Multiple replicate files

Issue - State: closed - Opened by tcolston almost 6 years ago - 2 comments

#12 - Bedgraph-ish files

Issue - State: closed - Opened by vanottee almost 6 years ago - 2 comments

#11 - Peaks failed to be detected

Issue - State: closed - Opened by dariober almost 6 years ago - 4 comments

#10 - About ATAC-seq

Issue - State: closed - Opened by AlexWanghaoming almost 6 years ago - 3 comments

#9 - About ATACseq mode (Large files, Warnings and p/q values)

Issue - State: closed - Opened by POTsnake almost 6 years ago - 9 comments
Labels: good first issue

#8 - single end data ATAC-seq mode

Issue - State: closed - Opened by ShuangHe33 almost 6 years ago - 2 comments

#7 - Segmentation fault (core dumped)

Issue - State: closed - Opened by ShuangHe33 almost 6 years ago - 10 comments

#6 - Sample has no analyzable fragments

Issue - State: closed - Opened by JulieHoang almost 6 years ago - 13 comments