jianhong ATACseqQC issues

jianhong / ATACseqQC

ATAC-seq Quality Control

https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html

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issues

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splitGAlignmentsByCut returns empty .bam files

#64 chklee30 opened 4 weeks ago
12
Error with splitGAlignmentsByCut

#63 chklee30 closed 4 weeks ago
1
question on the rationality of spliting the bam files

#62 sunta3iouxos closed 3 weeks ago
1
how do I read my shifted bam ad an obj in splitGalignmentsByCut

#61 sunta3iouxos opened 1 month ago
7
readBamFile with bigFile=TRUE still returns 0 GAlignmentsList

#60 sunta3iouxos opened 1 month ago
2
estimated library size of NucleosomeFree.bam is unexpectedly small

#59 cparsania opened 4 months ago
2
Clear loaded tracks in IGVSnapshot.R

#58 Sfeng666 closed 8 months ago
1
Optimizing Time and Memory Usage for Large BAM Files

#57 FarzanehRah opened 1 year ago
6
Error in TSSEscore calculation

#56 pai-vlc closed 1 year ago
15
should the original bam be deduped and chrM deleted for the analysis of fragSizeDist()?

#55 yjiakang closed 1 year ago
2
Interpreting the outputs of the function TSSEscore() comparing to the reference from ENCODE

#54 SergioRodLla opened 1 year ago
5
merge master to staging

#53 jianhong closed 2 years ago
0
Read the shifted bam and continue the QC analysis

#52 XiaoyuZhan520 opened 2 years ago
7
Output bam files become smaller after shiftGAlignmentsList

#51 Rui-Jing opened 2 years ago
4
different TSS.filter values affect the signals showing on the heatmap

#50 hyjforesight opened 2 years ago
1
NA values in sigs makes heatmap not completed

#49 hyjforesight closed 2 years ago
4
Error: subscript contains invalid names for splitGAlignmentsByCut() function

#48 hyjforesight closed 2 years ago
8
Strange TSS Enrichment Result

#47 astarr97 opened 2 years ago
1
What does the x axis mean for Nucleosome Free Regions (NFR) score plot?

#46 hyjforesight closed 2 years ago
3
Question about the read filtering by bamQC

#45 etiennedanis opened 3 years ago
1
Question about bamQC

#44 etiennedanis opened 3 years ago
1
Processing multiple bam files at once

#43 etiennedanis closed 3 years ago
2
splitBam fragment sizes for nucleosome-free DNA

#42 rauldiul opened 3 years ago
2
splitGAlignmentsByCut Error in value[[3L]](cond) : 'mergeBam' 'destination' exists, 'overwrite' is FALSE destination: splitBam/NucleosomeFree.bam

#41 rafet2005 opened 3 years ago
8
Problem with shiftGAlignmentsList()

#40 jingyu0602 opened 3 years ago
2
How do I read a BAM file？

#39 BeyondMyPast228 opened 4 years ago
1
splitBam return a asBam error

#38 jupollet opened 4 years ago
3
shiftGAlignmentsList() error

#37 hirokomatsui opened 4 years ago
1
CIGAR and query sequence are of different length, as.Bam truncated input

#36 csittz closed 4 years ago
0
plot correlation is not symmetric

#35 noorisotoudeh closed 4 years ago
1
estimateLibComplexity error

#34 noorisotoudeh opened 4 years ago
0
inconsistencies between the package code and user guide

#33 tinavisnovska closed 4 years ago
1
Error on running splitBam

#32 hchetia closed 3 years ago
13
Pls help with the error... I am using hg38

#31 hjack123 opened 4 years ago
1
adjusting readBamFile output for plotCorrelation

#30 tinavisnovska opened 4 years ago
4
factorFootprints error on system.file("extdata", "GL1.bam",package="ATACseqQC")

#29 tinavisnovska opened 4 years ago
2
phastCons100way.UCSC.hg19 equivalent for mm10 ?

#28 Just08 opened 4 years ago
7
Remove interactive() in readBamFile.R

#27 Puriney opened 4 years ago
0
Fix wrong index assgined in gal1

#26 ycl6 closed 3 years ago
4
error in factorFootprints function

#25 nevelsk90 closed 4 years ago
1
splitGAlignmentsByCut 'mergeBam' error

#24 GBeattie closed 4 years ago
7
A typo at readBamFile.Rd

#23 PollyTikhonova closed 4 years ago
1
shiftGAlignmentsList after samtools fixmate error

#22 Hdang1234 closed 4 years ago
14
Question about readBamFile function

#21 El-Castor opened 4 years ago
20
How to normalize cut-site probability between samples

#20 kshimizu64928 opened 4 years ago
0
error running factorFootprints -- evaluations nested too deeply

#19 magruca opened 4 years ago
0
treated as unmapped - splitGAlignmentsByCut

#18 yurasong opened 5 years ago
2
factorFootprints 'seqnames' issue

#17 mmilevskiy opened 5 years ago
5
TF footprint figure

#16 kshimizu64928 opened 5 years ago
0
shiftGAlignmentsList Error

#15 samiragarwala opened 5 years ago
3