Hi Admin, I used rmdup within samtools to remove duplicates for paired-end reads with default parameters, and met with this warning [bam_rmdup_core] inconsistent Bam file for pair “xxxxxx”. Continue anyway.
I have trimmed the fastq files according to known adapter, and kept the co-existing read pairs, so the length of read is shorter and may be different for mate 1 and 2 reads, then run mapping, sort the bam files by position. Is the warning caused by this trimming step? Thank you. Best, Li Qian ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
