Hey there,
I have been using tadpole for error correction (and BBtools in general) and I am extremely happy with its results and performance....
19 results in 0.0030 seconds.
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Run Tadpole (BBtools) only on sub-sets of reads from input files
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Error encountered when running kmercountexact.sh from bbmap
Hi all,
I am encountering a java.lang.AssertionError when trying to run kmercountexact.sh.
The two input files are 820 Mb... -
FastQC Report
I ran a HiSeq on environmental samples and the purpose of the run was to blast my sequences against the NCBI-nr database to see what species my reads... -
Weird overrepresented K-mers in FastQC
Hi! We have recently done the first run on a new NextSeq 500 machine which produced reads with weird FastQC results (attaching below).
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Odd Ray Error "Assembler panic: no k-mers found in reads."
Hi all,
I'm having an odd Ray error. I have a set of PE fastq files that are 35bp-101bp (confirmed through fastqc). When I run a Ray assembly... -
Why is predicted best k for de novo assembly so different from actual best k?
Greetings everyone,
I’m doing my first genome assembly for a non-model plant species, and I need some insight about best kmer lengths... -
Considering paradoxical assemblies and a question about repeat content estimation
Edit: to allow my question to be more useful to future researchers with similar questions, I've split my long, multi-paragraph series of questions into...Last edited by NYGen; 06-05-2015, 12:12 PM. Reason: Split long series of slightly-related but ultimately different questions into more-useful, smaller posts -
Heterozygous rate from "de novo" sequencing
Hi,
I've just tried to calculate the heterozygous rate of my seq data, but no luck using gce or even preqc from sga using kmer information.... -
Kmer spectrum insight requested
Hi,
I am hoping to gain some insight into my kmer spectra graphs, as many of them don't have the usual bi-modal distribution as I have... -
FastQC, Kmer count, Trimmomatic: no success in trimming, still fail Kmer
I'm using RNAseq for DGE and failed in trying to map paired end reads in TopHat2. Samples passed the first two parts of fastqc, but failed per base and... -
Is high Kmer coverage in PE reads, good?
Hi
I am doing de novo assembly of a bacterial genome, through paired end reads using velvet.
If I use Kmer length 75, in the Kmer coverage...Last edited by konika; 05-21-2014, 04:10 AM. -
Kmer spectrum
The kmer spectrum plots the number of distinct N-bp sequences as a function of coverage level, placing low-coverage (rare) sequences at... -
De novo assembly using Velvet: any idea why such small Kmers with long reads?
Greetings!
I am doing some de novo genome assembly of a 23Mb genome using Velvet 1.2.10 and quality trimmed MiSeq (Illumina) reads that average... -
fastqc Kmer Interpretation Help
Hi,
I've got some old Illumina RNA Seq data and there's an unusual trend in terms of Kmer detection. I have 16 samples done over two chips,... -
stange kmer content
hi all,
I've got this fastqc report with high ttttt all along the 1st group of paired-end reads, and high aaaaa &&. I TTTTT all along the...Last edited by MissDona; 01-04-2014, 05:55 PM.
