SOLID split RNA-Seq mapping

darked89

Member

Join Date: Jun 2009

Posts: 38
Share

Post
#1

SOLID split RNA-Seq mapping

08-15-2011, 06:23 AM

I got few SOLID RNA-Seq files which I am trying to map to some "draft+ quality" mammalian genome. So far I tried:

bowtie 0.12.7 (unspliced mode)
tophat 1.3.1 (spliced)
ab_wtp_1.2.1 (spliced)

Bowtie works OK but obviously misses spliced reads. Tophat without annotations maps less reads than bowtie. Whole Transcriptome Pipeline gives me colorspace gff file which then GffToSam fails to convert to SAM (error: "doesn't have F3 or R3 tag. Skipping.").

I wonder what is being currently used to map SOLID RNA-Seq data in spliced mode and get viewable in IGV SAM/BAM files in the end?

Any information about ab_wtp (or other software) config.ini files will be very helpful.
Tags: None

Previous template Next

Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool

by SEQadmin2

CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.¹ But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

Despite this, “CRISPR helped turn genome editing from a specialized technique into...
- Channel: Articles
Yesterday, 11:01 AM
Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications

by SEQadmin2

Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

The systematic characterization of the human proteome has...
- Channel: Articles
07-20-2026, 11:48 AM
Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM

Topics	Statistics	Last Post
New Genomic Method Uncovers Ancient Hominin DNA by SEQadmin2 Started by SEQadmin2, Yesterday, 02:55 AM	0 responses 9 views 0 reactions	Last Post by SEQadmin2 Yesterday, 02:55 AM
Study Captures the First Moments of DNA Replication by SEQadmin2 Started by SEQadmin2, 07-24-2026, 12:17 PM	0 responses 12 views 0 reactions	Last Post by SEQadmin2 07-24-2026, 12:17 PM
Chemotherapy Leaves Detectable DNA Signatures in Childhood Tumors by SEQadmin2 Started by SEQadmin2, 07-23-2026, 11:41 AM	0 responses 12 views 0 reactions	Last Post by SEQadmin2 07-23-2026, 11:41 AM
Single-Cell Atlases Skew Toward European Ancestry, Analysis Finds by SEQadmin2 Started by SEQadmin2, 07-20-2026, 11:10 AM	0 responses 24 views 0 reactions	Last Post by SEQadmin2 07-20-2026, 11:10 AM

Unconfigured Ad

SOLID split RNA-Seq mapping

Latest Articles

ad_right_rmr

News