I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried...
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Error when bbmapping RNA-seq data
Hello
I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried... -
Webinar: Perform large NGS assembly and analysis on any computer
Join DNASTAR Senior Product Manager Matthew Keyser to learn how to quickly assemble large NGS data sets using a simple laptop or desktop computer, including... -
Comparing RNA levels in tumor/normal samples using RNA-seq
Hi,
I'm starting a new cancer gene expression project using Illumina
RNA-seq fastq files for matched tumor/normal samples.
... -
Allelic Imbalance with GSNAP
Hi,
I'm working on creating simple pipeline for allelic imbalance analysis for our lab. We want to analyze allelic imbalance for F1 crosses... -
HISAT2 / hisat2_extract_snps_haplotypes_VCF.py / --genotype-vcf & VCF_fnames
Dear all,
I would like to use the Python script hisat2_extract_snps_haplotypes_VCF.py.
I cannot fully understand some of... -
Viral gene in data
hi,
I have some RNA-seq data for human cell line samples and one of them expresses a viral gene, I would like to map and quantify the data... -
Segemehl -Z option doesnt work with split read mapping
Hi,
My RNA-seq data has transcript fusions and novel splice-junctions. So, I am trying to use segemehl in local alignment (-S) mode to... -
Problem with the insert size of RNA-seq paired end reads!
The problem is that I cannot get a huge part of my RNA-seq data aligned!
These are some samples from the liver, intestine and colon of mice. We...Last edited by rozitaa; 02-24-2015, 05:21 AM. -
Improve accuracy of trinity RNA-Seq assemblies with --min_glue and/or --min_kmer_cov
Hi,
Does anyone know if it possible to improve the accuracy of Trinity RNA-Seq assemblies using --min_glue and/or --min_kmer_cov flags?
... -
Map with Tophat, DEGs with EdgeR. Possible?
Dear all,
Please some general and technical advice with the following. I would like to run edgeR as an alternative to cufflinks. I have... -
BBMap (aligner for DNA/RNAseq) is now open-source and available for download.
BBMap is now available here:
https://sourceforge.net/projects/bbmap/
Links to other BBTools forum threads:
BBSplit (Binning...Last edited by Brian Bushnell; 12-04-2016, 12:09 AM. -
RNA-Seq spliced aligners. Exon first vs Seed extend
Hi guys.
I was just wondering about some peoples opinions on RNA-Seq aligning methods. Maybe I'm misunderstanding it but I would think that... -
Comparison of RNA-Seq Aligners
Others seeing lower mapping yields using TopHot compared to other aligners?
Systematic evaluation of spliced alignment programs for RNA-seq...
