12 results in 0.0028 seconds.
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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... -
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. -
Optical duplicates Hiseq4000
Dear all,
I am working with RNA data sequenced on the Hiseq4000 sequencer. I am trying to quantify the number of "optical duplicates"... -
HS_LIBRARY_SIZE vs. ESTIMATED_LIBRARY_SIZE
Nothing came up on a search here today for me, so I dug into these Picard modules.
Looks like MarkDuplicates.ESTIMATED_LIBRARY_SIZE estimates... -
Picardtools MarkDuplicates Question
Hi all,
I am running Picardtools markduplicates, but when I start it running, I get the following error:
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some basic questions about duplicate removal ?
Hi all,
I am using the GATK pipeline for pre processing bam files after alignment with bwa mem. The original bam files after alignment... -
keep read address using tophat
Maybe overlooking something but ...
when I use tophat with paired reads having a name as
I end up with the second part clipped... -
samtools piping problem
Hello SEQanswers,
My ultimate goal is to pipe multiple different regions of a bam file to different commands in a single command line argument.... -
Mark duplicates after fastq trimming?
Hello!
I am fairly new to bioinformatics and have a question about using Picard Mark Duplicates after trimming Illumina sequence reads.
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Picard MarkDuplicates - whole bam file marked as duplicates
Hi,
I ran an RNA-Seq data set using the RUM-pipeline to align the data. I tried to use the Picard's MarkDuplicates - and it tagged very... -
Error with MarkDuplicates in Picard
Dear All
I am still on the learning curve with the GATK tool but I encountered an error at the duplicates marking step with Picard tool.
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Samtools's rmdup vs. Picard's MarkDuplicates
I am trying to remove duplicate using samtools's rmdup and rmdupse, they don't seem to just remove everything that share the same start/end sites. I...
