Hi
I would like to do strand specific mapping to a set of bacterial RNA-Seq files. The libraries were prepared using the KAPA hyperprep...
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Strand Specific mapping
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Questions about small RNA-seq (single-end and strand-specific)
Hello everyone!
I'm new analyzing transcriptomic.
I have small RNA-seq data, single-end from Rat.
Initially, I mapped the data with... -
featureCount overlapping features from different strands
Hi all,
My name is Haritz Irizar and I am a postdoctoral fellow at the Icahn School of Medicine at Mount Sinai.
I'm intending... -
Is ddRAD sequencing strand-specific?
Hi all,
I have ddRAD libraries that I am trying to build an assembly-based reference, but I am not sure if ddRADseq sequencing reads are... -
increased bias in single-buffer library preps (NEB, KAPA,...) Reason for concern?
Hi All,
the latest generation of library prep kits seem very convenient (only a single cleanup) and promise higher complexity sequencing... -
how to caculate rpkm for bacteria RNA-SEQ data?
hello, everyone! I am a new member here.
Recently, I am working with the bacterial RNA-SEQ data. My data was in strand-specific PE reads fq file.... -
Some "wrong" XS:A in Tophat output for strand specific pair-end RNA-Seq data
Hi, all,
When dealing with strand-specific pair-end RNA-Seq data, sequenced from 5' end and mapped with --library-type fr-secondstrand,... -
Tophat strand-specific RNAseq- Do i need to reverse-complement?
Hi all
I have strand-specific RNAseq data ( using Truseq kit- dUTP method) and I aligned the reads onto the genome with Tophat using --library-type=fr-firststrand... -
RNAseq strand-specific vs.non strand-specific
Hi there 'RNA-sequers',
I am pretty new to this field and I would like to ask (something maybe basic) if anyone could please explain to... -
Tophat2 in strand-specific mode: discrepancy between 0x10 bit and XS flag
Hi,
I've got single end RNA-seq reads coming from a strand-specific protocol. After running tophat2 v2.0.6 using the --library-type fr-firststrand... -
Lexogen has launched exceptionally strand-specific mRNA-Seq library prep kit
Lexogen, a Vienna-based transcriptomics and NGS company has launched a new SENSE mRNA-Seq stranded library prep kit. Exceptional strand-specificity (>99.9%)...Last edited by lexogen; 12-06-2012, 07:57 AM. -
Bowtie tags for dUTP strand specifc RNA-seq
Hello,
I'm new to this area and I just wanted to confirm I'm not missing out on something important. I have RNA-seq strand specific, single... -
Strand-specific Expression analysis in Cufflinks
I'm trying to use TopHat and Cufflinks mainly for differential gene expression analysis according to the protocol by Trapnell et al. (Differential gene... -
How should a strand-specific experiment look like in IGV?
I have a paired-end, strand-specific dataset and used Trinity to assemble the contigs. I then mapped the reads back to the contigs to calculate transcript... -
Mapping strand-specific data with TopHat
I have RNA-seq data that I want to map using TopHat. The library prep was done using ScriptSeq v2, and the sequencing using Illumina.
The...
