Chipseq peak analysis using ChIPseeker
1
Hi ,
I am using ChIPseeker tool for my Chipseq data analysis, But my heatmap of ChiP binding to TSS regions is almost blank “attached image”,
I used macs2 output file.
I used following commands:
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peak <- readPeakFile("chip_vs_input_summits.bed")
covplot(peak, weightCol="V5")
##Profile of ChIP peaks binding to TSS regions
promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
tagMatrix <- getTagMatrix(peak, windows=promoter)
tagHeatmap(tagMatrix, xlim=c(-3000, 3000), color="red")
genome
ChIP-Seq
chipseeker
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Warning message:
In .Seqinfo.mergexy(x, y) :
Each of the 2 combined objects has sequence levels not in the other:
The warning message is OK, as you can check:
> seqlevels(txdb)
[1] "chr1" "chr2" "chr3"
[4] "chr4" "chr5" "chr6"
[7] "chr7" "chr8" "chr9"
[10] "chr10" "chr11" "chr12"
[13] "chr13" "chr14" "chr15"
[16] "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21"
[22] "chr22" "chrX" "chrY"
[25] "chrM" "chr1_gl000191_random" "chr1_gl000192_random"
[28] "chr4_ctg9_hap1" "chr4_gl000193_random" "chr4_gl000194_random"
[31] "chr6_apd_hap1" "chr6_cox_hap2" "chr6_dbb_hap3"
[34] "chr6_mann_hap4" "chr6_mcf_hap5" "chr6_qbl_hap6"
[37] "chr6_ssto_hap7" "chr7_gl000195_random" "chr8_gl000196_random"
[40] "chr8_gl000197_random" "chr9_gl000198_random" "chr9_gl000199_random"
[43] "chr9_gl000200_random" "chr9_gl000201_random" "chr11_gl000202_random"
[46] "chr17_ctg5_hap1" "chr17_gl000203_random" "chr17_gl000204_random"
[49] "chr17_gl000205_random" "chr17_gl000206_random" "chr18_gl000207_random"
[52] "chr19_gl000208_random" "chr19_gl000209_random" "chr21_gl000210_random"
[55] "chrUn_gl000211" "chrUn_gl000212" "chrUn_gl000213"
[58] "chrUn_gl000214" "chrUn_gl000215" "chrUn_gl000216"
[61] "chrUn_gl000217" "chrUn_gl000218" "chrUn_gl000219"
[64] "chrUn_gl000220" "chrUn_gl000221" "chrUn_gl000222"
[67] "chrUn_gl000223" "chrUn_gl000224" "chrUn_gl000225"
[70] "chrUn_gl000226" "chrUn_gl000227" "chrUn_gl000228"
[73] "chrUn_gl000229" "chrUn_gl000230" "chrUn_gl000231"
[76] "chrUn_gl000232" "chrUn_gl000233" "chrUn_gl000234"
[79] "chrUn_gl000235" "chrUn_gl000236" "chrUn_gl000237"
[82] "chrUn_gl000238" "chrUn_gl000239" "chrUn_gl000240"
[85] "chrUn_gl000241" "chrUn_gl000242" "chrUn_gl000243"
[88] "chrUn_gl000244" "chrUn_gl000245" "chrUn_gl000246"
[91] "chrUn_gl000247" "chrUn_gl000248" "chrUn_gl000249"
> seqlevels(peak)
[1] "chr1" "chr1_random" "chr10" "chr11" "chr12"
[6] "chr13" "chr13_random" "chr14" "chr15" "chr16"
[11] "chr17" "chr18" "chr19" "chr2" "chr3"
[16] "chr4" "chr5" "chr6" "chr7" "chr8"
[21] "chr8_random" "chr9" "chrUn_random" "chrX" "chrY"
[26] "chrY_random"
I can produce the tagHeatmap using the sample bed file you provided.
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Sorry in above case I used peak summit file, now I tried with *peaks.narrowPeak macs2 output files,
when I used this file it gives some warnings:
maybe send me your bed file and source code for me to reproduce the issue.
Thanks,
this is my macs2 command:
macs2 callpeak -t chip.bam -c input.bam -f BAM -B -g hs -n rep1
and input bed file:
http://www.filedropper.com/showdownload.php/sample1peaks
or
http://s000.tinyupload.com/index.php?file_id=66463745037323321210