what the "mean original quality" and "mean quality" mean in the pdf output of MeanQualityByCycle tools of picard

Dear all,

I use picard tool MeanQualityByCycle to plot the quality distribution of bases. I wonder what the mean of "cycle", and what the difference of "mean original quality" and "mean quality"? Anyone can help me? Thank you.

Best,
Michael

next-gen alignment picard

• 1,770 views • link

updated 4.0 years ago by Ram

• written 10.7 years ago by zengxi.hada

0 answers

No answers yet.

More posts like this

multiple sequence alignmet
written 1.9 years ago by harry •

Dear all, please help me find the best tool for the nucleotide sequence alignment of the multiple sequences of the colourful and interactive publication quality …
Filter reads by calculating the distribution of phred score in each individual read
written 7.9 years ago by Nagesh •

Dear All, I would like to know if there is any tool or script to calculate the distribution of PHRED score for each individual read …
Is there any risk of having my research scooped after posting my manuscript onto bioRxiv ?
written 9.2 years ago by zengxi.hada

Dear all, I want to post my manuscript to bioRxiv before submitting onto formal journals, but I still have several concerns: 1. Can I claim …
The problem using samtools stats
written 9.3 years ago by 934963534 •

There is information of "ACGT content per cycle" What does the cycle mean? Also I see there are lines start with GCC and has the …
MEDIPS: Error: 1: Extra content at the end of the document
written 10.2 years ago by zengxi.hada

Hi, I encounter a error when run MEDIPS.getAnnotation in MEDIPS R package. Here are my command lines and error messages. I wonder why that happens …
what is input set in MEDIPS and how to create the bam file for INPUT SET?
written 10.2 years ago by zengxi.hada

Hi, I wonder what is the input set in MEDIPS and how to create the bam file for input set, as it's not described clearly …
How to change the default fold of the downloading sra data using prefetch ?
written 10.5 years ago by zengxi.hada

Hi, I am trying to use "prefetch" to download sra data. But I found the default output folder is `/home/[USER]/ncbi/public/sra/`, which is not big enough. …
what the "cycle" mean in MeanQualityByCycle of picard
written 10.7 years ago by zengxi.hada

Hi, I use picard tool "CollectBaseDistributionByCycle" to plot a figure "CollectBaseDistributionByCycle.pdf". But I have no idea about what's the mean of cycle of x lab. …
Mean read length
written 11.5 years ago by Korsocius

Dear all, I have one question. After sequencing I received mean read length distribution 121bp every time. In last two runs I received mean read …
P-values distribution meaning
written 11.9 years ago by Juan Cordero

Hi dear community, Could anyone tell me what changes in the p-value distribution mean? I mean, for example, what does mean that the p-values follow …