Matthias Munz

@sfchen Fastqc (Trimmed) refers to the output of Fastp which I ran only with default parameters. Sorry for the confusion. Has anyone else seen the same discrepancy between Fastqc and...

@sfchen Multiqc says that the Fastp duplication rate was calculated on the "filtered" reads which I understand as the reads outputted by Fastp. Am I understanding something wrong or is...

I think you missed this: I also checked the Fastqc duplication rate in the original (raw) data and it corresponds almost exactly with the Fastqc duplication rate after Fastp processing.

I see the point. I am also quite busy right now, but I can extend the error message and link a script which adds the missing fields. Just have to...

Hello @zhanxw, I am getting exactly the same error as @sbaheti. Here is an example to reproduce the error: refFlat.txt ``` SLMAP NM_007159 chr3 + 57757255 57930016 57757651 57927388 21...

@ayub1985 found out that the program cannot handle vcf files properly if there is "chr" before the chromosome number for the variants.

+1