Question: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
0
gravatar for mbasam
4 months ago by
mbasam0
mbasam0 wrote:

When trying to use ATACseqQC on a larger bamfile, I receive the following error:

Error in .local(x, ...) : strand values must be in '+' '-' '*' Calls: splitGAlignmentsByCut ... normalizestrandreplacement_value -> strand -> strand -> .local

I checked the structure of the bamfile using str(gal) and under strand values I see: Factor w/ 3 levels "+","-","*": 3.

The bamfile is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/112R-rep1-chr1-bwa.bam

The R script is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R

The log file that shows the full error is available to be downloaded here: http://s3.amazonaws.com/mudaser/bamfiles/Heatmap.log

Any insight would be much appreciated.

(Ideally, I would like to use the entire bamfile without limiting to chr1, but we received separate errors that I may make another post about at a later time).

R atacseqqc • 182 views
ADD COMMENTlink modified 4 months ago by Julie Zhu4.1k • written 4 months ago by mbasam0
Answer: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
0
gravatar for Julie Zhu
4 months ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:

Could you please share your session information with us? The most recent release of ATACseqQC is 1.8.1 (https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html). Thanks!

Best regards, Julie

ADD COMMENTlink written 4 months ago by Julie Zhu4.1k

Hi Julie,

I have the most recent version of ATACseqQC (1.8.1) installed. Here is the session info:

R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /opt/R/3.6.0-Python-3.6.6-foss-2018b/lib64/R/lib/libRblas.so LAPACK: /opt/R/3.6.0-Python-3.6.6-foss-2018b/lib64/R/lib/libRlapack.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LC
TIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LC
MONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LC
PAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] BSgenome.Hsapiens.UCSC.hg191.4.0
[2] BSgenome
1.52.0
[3] rtracklayer1.44.0
[4] TxDb.Hsapiens.UCSC.hg19.knownGene
3.2.2 [5] GenomicFeatures1.36.1
[6] AnnotationDbi
1.46.0
[7] Biobase2.44.0
[8] phastCons100way.UCSC.hg19
3.7.2
[9] GenomicScores1.8.0
[10] Rsamtools
2.0.0
[11] Biostrings2.52.0
[12] XVector
0.24.0
[13] GenomicRanges1.36.0
[14] GenomeInfoDb
1.20.0
[15] IRanges2.18.1
[16] ATACseqQC
1.8.1
[17] S4Vectors0.22.0
[18] BiocGenerics
0.30.0

loaded via a namespace (and not attached): [1] ProtGenerics1.16.0 bitops1.0-6
[3] matrixStats0.54.0 bit640.9-7
[5] progress1.2.2 httr1.4.0
[7] tools3.6.0 rGADEM2.32.0
[9] R62.4.0 KernSmooth2.23-15
[11] seqLogo1.50.0 colorspace1.4-1
[13] DBI1.0.0 lazyeval0.2.2
[15] ade41.7-13 motifStack1.28.0
[17] tidyselect0.2.5 prettyunits1.0.2
[19] grImport20.1-5 bit1.1-14
[21] curl3.3 compiler3.6.0
[23] VennDiagram1.6.20 graph1.62.0
[25] formatR1.6 DelayedArray0.10.0
[27] scales1.0.0 randomForest4.6-14
[29] RBGL1.60.0 rappdirs0.3.1
[31] stringr1.4.0 digest0.6.19
[33] jpeg0.1-8 base64enc0.1-3
[35] pkgconfig2.0.2 htmltools0.3.6
[37] dbplyr1.4.1 ensembldb2.8.0
[39] limma3.40.2 regioneR1.16.2
[41] htmlwidgets1.3 rlang0.3.4
[43] RSQLite2.1.1 shiny1.3.2
[45] BiocParallel1.18.0 dplyr0.8.1
[47] RCurl1.95-4.12 magrittr1.5
[49] polynom1.4-0 GO.db3.8.2
[51] GenomeInfoDbData1.2.1 futile.logger1.4.3
[53] Matrix1.2-17 munsell0.5.0
[55] Rcpp1.0.1 stringi1.4.3
[57] yaml2.2.0 edgeR3.26.4
[59] MASS7.3-51.4 SummarizedExperiment1.14.0
[61] zlibbioc1.30.0 BiocFileCache1.8.0
[63] AnnotationHub2.16.0 grid3.6.0
[65] blob1.1.1 promises1.0.1
[67] crayon1.3.4 lattice0.20-38
[69] splines3.6.0 multtest2.40.0
[71] hms0.4.2 locfit1.5-9.1
[73] pillar1.4.1 MotIV1.40.0
[75] seqinr3.4-5 biomaRt2.40.0
[77] futile.options1.0.1 XML3.98-1.20
[79] glue1.3.1 lambda.r1.2.3
[81] BiocManager1.30.4 idr1.2
[83] png0.1-7 httpuv1.5.1
[85] purrr0.3.2 assertthat0.2.1
[87] mime0.6 preseqR4.0.0
[89] xtable1.8-4 AnnotationFilter1.8.0
[91] later0.8.0 survival2.44-1.1
[93] ChIPpeakAnno3.18.1 tibble2.1.3
[95] GenomicAlignments1.20.0 memoise1.1.0
[97] interactiveDisplayBase_1.22.0

ADD REPLYlink written 4 months ago by mbasam0

Thanks! The main developer Jianhong will work on it and post the solutions here. Best regards, Julie

ADD REPLYlink written 4 months ago by Julie Zhu4.1k

I am wondering whether you could run the examples at https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html, and whether you have the index file 112R-rep1-chr1-bwa.bam.bai in the same directory as 112R-rep1-chr1-bwa.bam file. Best regards, Julie

ADD REPLYlink written 3 months ago by Julie Zhu4.1k

I made it by myself. I just cannot repeat the error yet. I am looking for the difference of secession info.

Best!

Your sincerely,

Jianhong Ou

On Jul 22, 2019, at 10:18 AM, Julie Zhu [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=Qe-NKzG8TfbjMso7g2ZuhEkm-_JqP1UrrdVWbPWFkw4&e=

User Julie Zhuhttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_3596_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=yAbAo2DHcn9YWRzqOyREA8USelr30NuT7UFC8bnGH5Y&e= wrote Comment: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_122844_-23123059&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=4pbH5yGWCb2BNHngqlP7AV0vo8QB3PwxW9MciqvFaQg&e=:

I am wondering whether you could run the examples at https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_vignettes_ATACseqQC_inst_doc_ATACseqQC.html&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ypYXViGpe99gxXOP31b2PHQTpVp93USZzlLqX9HHhf4&s=r-0RyxoJMC9hk22Iq1kGacSMYOqXz1zOZL2amOGTMd4&e=, and whether you have the index file 112R-rep1-chr1-bwa.bam.bai in the same directory as 112R-rep1-chr1-bwa.bam file. Best regards, Julie

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k

Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you?

ADD REPLYlink written 3 months ago by mbasam0

Hi, yes the files are in the same directory. That is interesting, so when you tried to test it, it worked for you?

ADD REPLYlink written 3 months ago by mbasam0
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