OpenGene
Mismatched UMI of a pair of reads
hello, I meet some mistake with the gencore (Version: 0.17.2): 1 contigs in the bam file: chr1: 7249 bp
Mismatched UMI of a pair of reads
Left:
0:0, M:0:0 TLEN:0 ID:0
E100030802L1C001R00101395324:umi_CA_NN
TTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTATTATTAATATTATTATTAATTTTAAAATCACAACAAAATACAAAAAACAAAAAAAAAAA
GGGGGHHGGHIGGGGGHGGGIIGGGGGGGGGGIGGGGHGIHGGGGGGHGGGGGGGGIGGGGGGHGGGHIGIGGGGGIIGGHHGGGGHIGGHG
Right:
0:0, M:0:0 TLEN:0 ID:0
E100030802L1C004R03200085905:umi_CG_NN
TTAAAAAATTATAAAAAAAAAATAAAAAAATAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
ERROR: The UMI of a read pair should be identical, but we got CA_ and CG_
but, when i find the reads in original bam ,the reads pair seem to be correct with same UMI :
it's seem like the gencore consider the two read with different read name to be one pair read.
the command is: gencore --umi_prefix=umi -s 3 --ref hg19.fasta --quit_after_contig 25 -i input.bam -o output.umi.bam
but when I add the "-d" parameter,there is no mistake , maybe there has some difference,: gencore --umi_prefix=umi -d 0 -s 3 --ref hg19.fasta --quit_after_contig 25 -i input.bam -o output.umi.bam
Looking forward to your reply!
I have met the same problem, looking forward other response.
Besides, I have tried the following method to solve it: before running the genecore , add this cmd: samtools view -@ $threads -bh -f 2 in.bam > out.bam to remove the unpair reads, and it works ok.
