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rita.monteiro
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@ritamonteiro-23554
Last seen 4.5 years ago
Hi,
I've been trying for over a week to run ATACseqQC on my data with little success. I managed to generate the shifted.bam file but I cannot split them into different categories based on fragment size. I managed to ran the package using the example samples and I think ( I'm sure at this point after so many trials) that I managed to do it with a subsample (Chr1) of data.
Here's the code and the error that I get:
packageVersion("ATACseqQC")
[1] '1.10.4'
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
library(ChIPpeakAnno)
library(Rsamtools)
library(GenomicRanges)
library(GenomicScores)
bamfile <- "*.bam"
bamfile.labels <- gsub(".bam", "", basename(bamfile))
outPath <- "./2h_B2_Test"
dir.create(outPath)
possibleTag <- combn(LETTERS, 2)
possibleTag <- c(paste0(possibleTag[1, ], possibleTag[2, ]),
paste0(possibleTag[2, ], possibleTag[1, ]))
bamTop100 <- scanBam(BamFile(bamfile, yieldSize = 100),
param = ScanBamParam(tag=possibleTag))[[1]]$tag
tags <- names(bamTop100)[lengths(bamTop100)==100]
seqlev <-(c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chrX","chrY"))
which <- as(seqinfo(Mmusculus)[seqlev], "GRanges")
genome <- Mmusculus
txs <- transcripts(TxDb.Mmusculus.UCSC.mm10.knownGene)
gal <- readBamFile(bamfile, tag=tags, asMates=TRUE, which = which, bigFile=TRUE)
shiftedBamfile <- file.path(outPath, "shifted.bam")
gal1 <- shiftGAlignmentsList(gal, outbam=shiftedBamfile)
objs <- splitGAlignmentsByCut(gal1, txs=txs, genome=genome, outPath = outPath)
And here's the error:
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:1:13208:3290:2190" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:1:22303:21110:16221" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:13112:7733:15765" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:4:11601:9523:4754" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:4:13606:5705:12385" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:3:22511:22886:7021" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:12208:11077:15338" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:3:23507:19885:11109" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:1:22204:5857:1791" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:4:21511:7543:2465" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:3:23408:6559:11844" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:3:13502:3326:18935" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:22102:9488:3937" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:1:12202:22122:12780" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:11209:3361:14587" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:13103:9747:4114" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:1:12207:23014:16371" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:3:11508:8191:4892" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:21101:10496:13188" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:2:11310:18186:7800" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "NB501779:62:HG3TYBGX5:4:23509:16389:11592" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[E::sam_parse1] unrecognized type N
[W::sam_read1] Parse error at line 22
[E::sam_parse1] unrecognized type N
[W::sam_read1] Parse error at line 22
[E::sam_parse1] unrecognized type N
[W::sam_read1] Parse error at line 22
[E::sam_parse1] unrecognized type N
[W::sam_read1] Parse error at line 22
[E::sam_parse1] unrecognized type N
[W::sam_read1] Parse error at line 22
[E::sam_parse1] unrecognized type N
[W::sam_read1] Parse error at line 22
[...]
Hi Rita,
Thank you for trying ATACseqQC to analyze your ATAC-seq data. This is a known issue that when one or more tags are missing, NA value will be generated when write it to sam file, which in turn trigger the error when convert sam file to bam file. Could you try it first by removing PG tag from your tags like this:
tags <- tags[tags!="PG"]
Let me know if you still have trouble.
I am planning to rewrite the export function when there is NA values.
Jianhong.
Hi Jianhong,
Thank you so much, it fixed the problem!
I'm running into another error when trying to plot the heatmaps and the normalised signals. When I run this code:
I get this error:
Do you have any tips on how to solve this?
Thanks again
Hi,
Did you see the heatmap? I did not see the error message from your description. I only see the warning message. Could you please show me the error message?
Jianhong.
Hi, Running the command I don't get any heatmap. I get the warning messages and there is no output. I've tried the code more times with different files and I keep getting the error. I don't know what I'm doing wrong.
Thank you.
Hi, Could you share your sigs.log2 and TSS object to me? I will check what happened.
Jianhong.