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High Duplication levels
I am looking at some bacterial Illumina RNA-seq data and seeing very high levels of sequence duplication. Inspecting the alignments on IGV revealed alignments... -
Help with FastQC results
Hi,
I have two sets of Illumina Single End RNA-Seq 50 bp data (two differents days of mammalian cell culture). The kit used was KAPA Stranded RNA-Seq... -
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. -
Anyone know a program to detect duplicated regions?
Hi All,
I'm working with on generating denovo mtDNA genomes for many species of an invertebrate taxa of the same genus. These critters... -
Duplication levels
Hello all,
I'm currently analyzing a single-end 50bp-read RNAseq data, which was sequenced at an outside facility. I've got a very naive question,... -
Strange strand bias and unusual depths
Hi all,
I'm seeing some very strange stuff with a resequenced prokaryotic genome coming from an Illumina HiSeq 2000. The design is 50bp... -
Problem with FASTQC on Trinity Mouse DC reads example dataset
Dear SEQanswers,
My name is Alex SMITH and I've recently started a RNA-seq bioinformatics post-doc at the Malaghan Institute of... -
FastQC Report: A horn in Per sequence GC content ?!
Hi Everyone,
Nice to meet you guys here!
I'm doing ChIP-Seq using HiSeq 1500 on SR 50 cycles, multiplexed condition.
And... -
SSPACE creates tandem duplications instead of merging
Hi all,
I'm using SSPACE v2.0 on a set of contigs assembled through Velvet, with parameters
-x = 0
-z =... -
Picard MergeSamFiles resulting in read duplication and loss of pair information
Hi,
I have merged some bam alignment files of different samples having read group information using picard's MergeSamFiles program.... -
fastqc sequence duplication level
Hi,
I was wondering if it is normal to have a fastqc plot with sequence duplication level around 60% for a high depth human exome sequencing... -
Exon duplication & deletions
Hi,
We're soon to be getting a MiSeq and one of our first projects is to look at a small number of genes for a large number of patients.... -
identification of indels/duplications up to 20 bp
Hi,
Is it possible to identify insertions, deletion or duplications of up to 20 bp with target enrichment and Illumina sequencing?
What... -
High duplication levels in FASTQC
Hi,
I was using FASTQC to QC my directional mRNA-Seq data obtained from suspension culture cells. I have about 30 million reads.
...
