60 results in 0.0026 seconds.
-
Confusing Picard HsMetrics ON_BAIT_VS_SELECTED for near=250 and near=0
Hi, for an assay developed by my vendor, I ran latest Picard HsMetrics (2.21.8) with two different options for the same set of BAM files: one with a NEAR_DISTANCE=250... -
Picard InsertSizeMetrics Output Interpretation
Hi,
I am looking at the data from my pilot Miseq Nano run performed on ATAC-seq libraries.
I wanted to see whether the fragment... -
Exact duplicate reads/readnames/quality/tiles in Novaseq FASTQs
Anyone seen this? Some (not correlated with software versions AFAICT) of our MarkDuplicates jobs are failing because there are exact copies of the same... -
BAM -> FASTQ why can I not produce the same result?
Dear all, I've been trying to test if I can produce the same fusion call starting from BAM instead of FASQ. My STAR command is as such.
... -
Dictionary size problem in Picard HsMetrics
Hi everyone,
I'm following a Roche pipeline for the analysis of targeted bisulfite sequencing data and I'm in trouble with Picard CalculateHsMetrics.... -
mark duplicates option
Hello. I would like to use MarkDuplicates of Picard, but I don't know how I should use the options. Could anyone give me an example of this .txt file?... -
Confused about RG ID LB even after reading all posts/GATK best practices
I am getting conflicting information on how to assign RG ID, LB, PU, SM for an exome analysis I am working with.
Can someone just clarify...Last edited by Studentlost; 03-05-2016, 08:06 PM. -
Picard IlluminaBasecallsToSam: Read Structure
Hi,
I am trying to convert MiSeq .bcl files into uSAM with Picard tools 'CheckIlluminaDirectory', 'ExtractIlluminaBarcodes' and 'IlluminaBasecallsToSam'.... -
fastq2bam
Hi,
which tools is better to convert fastq2bam? picard or samtools or any other that you may suggest? it seems that picard has different converters... -
Cannot add sequence that already exists in SAMSequenceDictionary
I am just learning how to analyse data
this is my steps
1. download library, combine them into single csv file by CRISPR.sgRNA_create_ref_fasta... -
Problem replacing contigs in a dbsnp vcf using Picard SortVcf
Right now I'm trying to change the contigs in the dbsnp vcf to match those of my reference genome (from 1, 2, ..., Y, MT to chrM, chr1, chr2,...)
... -
Is read duplication the wrong metric?
My collaborator had some libraries sequenced much more deeply after the initial results seemed too shallow, but the total read counts per library were...Last edited by jwfoley; 01-19-2015, 10:53 AM. -
Picard, Markduplicates
We use Picard/CleanSama.jar:
java -Xmx4g -jar $Picard_jarFolder/CleanSam.jar INPUT=$sample OUTPUT=$clean_picard VALIDATION_STRINGENCY=LENIENT... -
preseq works on deduplicated BAM files?
please ignore this thread, error was caused by a difficult to spot bug in my own code. -
Picardtools MarkDuplicates Question
Hi all,
I am running Picardtools markduplicates, but when I start it running, I get the following error:
...
