Hi all,
I'd like to share a modular and transparent bash-based pipeline I’ve developed for pre-processing ddRADseq Illumina paired-end...
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Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and de-duplication using cutadapt
Last edited by rafalwoycicki; 04-23-2025, 06:10 AM. -
Find out if you have amplicon reads.
Is there really no way (program, tool) to tell if your BAM files have amplicon reads?
How is everyone doing it? determining a priori and... -
Interpretation of bwa output - has it used all the reads
I am analyzing an RNASeq data set. I have screened reads in Trimmomatic and aligned them using bwa mem. The reads are mostly 100bp long, but a minority... -
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... -
Comparing RNA-seq libraries with different levels of PCR duplication
Hi all,
We are analyzing a set of RNA-seq libraries and noticed that our libraries have very different levels of PCR duplicates, resulting... -
How does BWA identify PCR duplicates correctly?
Does it use the usual "same-start-position-for-both-paired-ends" approach? If so, why do many users do this check manually or use picard and... -
Ion torrent PCR duplicates
Hi All,
I am looking at some targeted ion torrent sequencing data. Over 90% of mapped reads are PCR duplicates. Is this normal? I thought... -
dulpicate reads from ampicon/PCR based library
I am having trouble getting my head round the issue of duplicate reads and in particular how this works with data derived from a amplicon generated PCR...Last edited by yog77; 07-30-2012, 03:28 AM. -
How can I parse these reads
...Code::::::::::::::: 0H.ptFlagstat.txt :::::::::::::: 49080460 + 0 in total 0 + 0 duplicates 6444347 + 0 mapped (13.13%:nan%)
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yksikaksi started a topic What is the differences between pre-filtering vs PCR duplicates remove mapped reads?in SOLiDWhat is the differences between pre-filtering vs PCR duplicates remove mapped reads?
Hello,
Does is a must to preform pre-filtering for color space reads before mapping?
Could it has a big differences in... -
Cufflinks v 1.2.0 high number of RPKM 0
I have three SOLiD human RNA-Seq libraries which I am analysing using cuffdiff. The libraries have a large number of reads which MAY be pcr duplicates... -
Picard Mark Duplicates help please
I am tying to use Picard MarkDuplicates to remove my pcr duplicates from a human rna-seq bam file. The run was paired-end but I only have about 30% properly... -
PCR duplicates increase when excess of beads
Hello,
We are experiencing an increasing of PCR duplicates.
Could this be realated to an increasing of the quantity of beads in order to...
