17 results in 0.0042 seconds.
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Dedupe on Geneious Prime
Hello. I am currently running Dedupe, a part of the BBTools plug-in on Geneious Prime, to remove duplicate reads. I have read that Dedupe detects and... -
Remove duplicate genes/mRNA from a gff file
I would like to combine two different gff files and then remove some duplicate genes/mRNA/exons with overlaps. I did not find any tool to do it. There... -
Picard MarkDuplicates and Secondary Reads
Hi all,
I am running picard MarkDuplicates with REMOVE_DUPLICATES=TRUE.
From what I have read, if picard marks a primary alignment...Last edited by Ham.m; 03-28-2017, 05:56 AM. -
Removing duplicate PacBio reads
Hi all,
I think the thread title says it all but below are a bit more details about my problem:
I have used PacBio sequence...Last edited by AgatheJ; 02-13-2017, 05:00 AM. -
Duplicate read names - BWA mem - paired reads have different names
Hi,
running BWA mem (- PE; - Illumina), I'm getting the following error (replaced the ids):
[mem_sam_pe]... -
Panel DNA data Remove Duplicates
Hi,all
We are doing panel data for variants calling and need to make it clear whether we should remove the duplicates with picard, I do... -
what happens with read duplicates?
I routinely mark (I do not delete) my duplicate reads using Picard MarkDuplicate wether I do gDNA seq or RNA Seq but I still ignore (besides for GATK)... -
To remove or to keep duplicates in alignment of NGS paired reads to a set of contigs
I have a SAM file containing alignments of NGS paired reads against a set of assembled contigs (de novo).
If I might need to infer some... -
preseq works on deduplicated BAM files?
please ignore this thread, error was caused by a difficult to spot bug in my own code. -
"Bcftools mpileup" removes marked duplicates?
Hey,
My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates?
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Removing Duplicates Scenario Exome Resequencing
I am rethinking my well-established pipeline and trying to tweek it a bit and came across some controversy on the use of remove duplicates. I would like... -
WGA and Duplicate Reads
We recently ran a sequencing experiment of tumor samples that where we needed to perform whole genome amplification (WGA) due to low amounts of tumor... -
Duplicates percentage in target resequencing
Hi,
We are performing a target resequencing experiment, where we enriched 8 regions.- What's the mean % of duplicates in this kind of
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A really bad library?
Hi guys,
I am a beginner in the data analysis of experiments RNASeq.
I am currently trying to align reads (36 bp) from an RNASeq experiment... -
Problem removing duplicate reads? (samtools and picard)
Hello,
I am having trouble removing duplicate reads with samtools and picard. I have a sam/bam file that is of paired-end illumina reads...
