PICARD AlignmentSummaryMetrics for RNA-Seq
1
0
Entering edit mode
7.6 years ago
rachanaj • 0

Hi

I used the following command to gather summary metrics for my bam file generated via bowtie2 (tophat to be specific):

java -jar /usr/share/picard-tools-1.136/picard.jar CollectAlignmentSummaryMetrics INPUT=Sample_DY10.tophat.bam OUTPUT=tmpmetrics/alignmentmetrics R=/mnt/storage/ref_genome/Homo_sapiens/UCSC_hg19/UCSC/hg19/Sequence/Bowtie2Index/genome.fa

The output file is here: https://drive.google.com/file/d/0B2tk2ztVP7NIa1NNM2FrMi1WSjg/view?usp=sharing

The question I have is that the metrics PF_HQ_MEDIAN_MISMATCHES has a very high number (66). When I look at NM tag in the bam file, I see that the median is 1 with max NM = 2 I am wondering how this number is calculated by PICARD.

Any help is appreciated.

PICARD RNA-Seq AlignmentSummaryMetrics • 2.5k views
ADD COMMENT
0
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 1333 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6