I started to work with cn-mops, but got all the time the same Error, after I start the program:
library(ggplot2) library(cn.mops) BAMFiles <- list.files(pattern=".bam$") bamDataRanges <- getReadCountsFromBAM(BAMFiles, mode="unpaired") Identified the following reference sequences: chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM Missing "refSeqName"! Selecting chr1 as reference sequence. Note that this function is much faster, if the indices of the BAM files are present. Missing "WL"! cn.mops will suggest an appropiate value for the window length. Window length set to: 197000 Reading file: 1_V22_T21_12P.bam chr1 Reading file: 2_V22_T18_12P.bam chr1
So I looked at the header of my BAM-Files, which look like this:
@HD VN:1.4 SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566......
and saw, that I really have no refSeqName in my Bam Header. Any Ideas how I can add the "refSeqName" and how it has to look like? for example:
"@HD VN:1.4 SO:coordinateref SeqName: hg19"
Thanks for your help! Karim