We’re organizing our annual Berlin Summer School in NGS Data Analysis (June 15-19, 2026), and thought it may be of interest to this...
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10th Berlin Summer School in NGS Data Analysis (July 2026, in-person, Berlin) – registration open
Hi all,
We’re organizing our annual Berlin Summer School in NGS Data Analysis (June 15-19, 2026), and thought it may be of interest to this... -
Registration OPEN: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024)
8th Berlin Summer School in NGS Data Analysis
When? June 10-14. 2024
Where? Berlin, Germany
Link? www.e... -
Tophat-fusion: Joining segment hits - FAILED
Hi,
I have been aligning RNAseq data using tophat-fusion for downstream analysis of circularRNA using CIRCexplorer2 (requires tophat-fusion... -
Tophat-fusion: Joining segment hits - FAILED
Hi,
I have been aligning RNAseq data using tophat-fusion for downstream analysis of circularRNA using CIRCexplorer2 (requires tophat-fusion... -
Tophat error
I am new to RNAseq, I am trying to map my reads to my reference genome. It generates this error
Generating SAM header for /path/ref
Traceback... -
Tophat2 alignment problem
I ran this code using tophat (v2.1.0) to align reads (bowtie2 (v2.2.6.0)) from my RNA-seq fastq file using the bowtie2 genomes.bt2 indexes from igenomes... -
Hisat2 vs Tophat2 variation between tech reps
I have a question regarding the variability of FPKM I am seeing between technical replicates in the Hisat2, stringtie pipeline. When I plot technical... -
tophat-fusion result
Can I use the accepted_hits.bam of "tophat2 --fusion-search" to calculate the gene expression level?
Usually I just use tophat... -
Tophat for filtering of stranded library
Dear all,
I want to use Tophat to filter out reads of the human host from my stranded RNA-seq library. Since I want to remove both sense... -
Fusion reads in BAM
I have BAM files which were run with tophat and --fusion-search --fusion-min-dist 1000000 --fusion-read-mismatches 2 --fusion-multireads 1 --fusion-multipairs... -
TopHat (Tuxedo Suite) - AWS vs Local
Hello All
Sorry this one's a bit long
Have come here after some testing !!
I am trying to run Tuxedo suite for RNASeq Analysis... -
How to create a GTF/GFF file for HTSeq OR how to count reads without GTF?
I am working with RNAseq of an insect under different treatments. I already have the data (Illumina HiSeq paired-end reads) and I was planning to follow... -
Help with TOPHAT on genepattern
Hello everyone!
I am new to bioinformatics. With a strong background in molecular biology and biochemistry, I am looking to transition... -
Different alignment rate of Tophat with and without GTF file
Hi,
I am new to RNA seq analysis. I am working on non-model organism. I have Genome and de-novo-assembled transcriptome. Using PASA I mapped... -
Tophat chromosome position greater than chromosome size
I use tophat to map the rna-seq reads (paired-end). It seems that some of the reads in the .sam do not make sense. Please see some examples below:...
