jianhong
commented
4 years ago Hi Hiroko,
Thank you for reporting this issue. I am writing the new export method to replace the export method in rtracklayer. The issue should be fixed in next building. Let me know if it still not work in development version 1.15.2 or in release version 1.14.2
Jianhong.
Hello,
I've been running the function and see following error many times: [bam_translate] RG tag "1" on read "K00180:164:HCG3YBBXX:2:1207:28057:2879" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] RG tag "1" on read "K00180:164:HCG3YBBXX:2:1124:23084:46627" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
The input bam file has @RG header with ID:1 Is there any way to output RG tags correctly. I'm running the following R commands:
library(ATACseqQC) library(Rsamtools)
bamfile tags to be read in
possibleTag <- combn(LETTERS, 2) possibleTag <- c(paste0(possibleTag[1, ], possibleTag[2, ]), paste0(possibleTag[2, ], possibleTag[1, ])) bamTop100 <- scanBam(BamFile(in_bam, yieldSize = 100), param = ScanBamParam(tag=possibleTag))[[1]]$tag tags <- names(bamTop100)[lengths(bamTop100)==100]
shift the coordinates of 5'ends of alignments in the bam file
gal <- readBamFile(in_bam, tag=tags, asMates=T, bigFile=T) shiftGAlignmentsList(gal, outbam=out_bam)
Thank you, Hiroko