I have a RNASeq fastq file (first 4 lines are):
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@SRR179591.1.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_58_235_F3 length=50
T.33.2010.0313.1231222320.1.3312.0.12.0212.0.013000...
16 results in 0.0031 seconds.
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Can Trimmomatic handle Colorspace Reads
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Tophat and Mapping QV
Hi,
I'm using TopHat v1.4.1 in order to analyze paired-end reads (75-35) in color space.
My tipical command line is:
tophat -G ... -
Mapping to colorspace genomes
I tried playing around with mapping of SOLID reads in colorspace and letterspace, and the two do not look even slightly alike.
The mapping...Last edited by tir_al; 09-11-2012, 07:09 PM. -
Columbus, Velvet color space SOLiD support
Hello, I want to assemble de novo SOLiD data with velvet but with fasta and sam references. Does anyone know if Columbus from Velvet supports color space?... -
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... -
Do I have to install velvet twice to run color and base space?
Hello, I want to install velvet to run sometimes sequence space (454), some times color space (SOLiD), and sometimes both.I see that in the installation... -
SOLiD seq process: Covert colorspace to basespace
I have a collection of colorspace solid sequences to be translated into basespace sequences. After view the post http://seqanswers.com/forums/showthr...Last edited by zhigangwu; 12-08-2011, 11:03 AM. -
which is the right conversion for Solid?
Hi, I have been using several scripts from maq, fastq-mcf and galaxy to transform my csfasta & qual data into fastq (in base space). all of them gave... -
Bfast Fatal Error during indexing
Hi,
I am trying to index a fastafile with the human genome (build GRCh37, only chromosomes + MT) using bfast. In color space.
I... -
colorspace data
hi, does anyone know of files out there that exist that have assembled genomes in colorspace, along with the qualities? I would imagine that it would... -
assembled whole genome colorspace files with qualities?
hi, are there files out there that exist that have assembled genomes in colorspace, along with the qualities? I would imagine that it would be in something... -
samtools colorspace calmd is incredibly slow
Hi all,
I'm running samtools version 0.1.14 (and bwa version 0.5.8c) and I am
trying to do solid colorspace analysis on some single-end... -
cutadapt: A tool that removes adapter sequences
I'm pleased to announce the tool 'cutadapt', which we have been using in our research group for adapter removal in high-throughput sequencing data. Removing... -
bwa question: quality discrepancy between a color-space alignment and its csfastq
I am using bwa to perform color-space alignments. I found that the quality line of a mapped read is totally different from its original value in the csfastq... -
BFast index creation & other SOLiD difficulties
Hi all,
I've been having lots of trouble getting 36 million SOLiD reads aligned to hg18. I started using bwa, but less than 40% of my...
