46 results in 0.0035 seconds.
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HTSeq-count: proper pairs in bam file
I have human RNA reads that I aligned against the human reference genome (GRCh 38) using BWA MEM and TopHat2. I now want to count the genes with HTSeq-count.... -
Looking for a good Riboseq analysis protocol
Hi all,
I am trying to analyze RNA_seq data for the first time and I am very confused.
I am looking for a good protocol I can trust..... -
TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file
I'm running TopHat v2.1.1 on Mycobacterium tuberculosis genome using the gtf file download from the EnsemblBacteria FTP. When trying map to genome I get... -
Issue with Htseq-count on BAM files from Tophat2 using Galaxy
Hello,
I'm currently facing troubles using galaxy. I want to compare differentially expressed genes between two treatment groups. I already... -
hisat2 multiple thread usage
Hello all, I am trying to switch over to using hisat2 instead of tophat. I have a couple questions:
1. It seems that we are able to input... -
Tophat2 chose a match with a deletion over one without
I'm a bit mystified by Tophat's (v2.1.0) choice of alignment in a case where I've got two similar genomes placed end to end (B73 and W22 maize) and I'm... -
tophat gene information
Hi all!
I used tophat2 with the option -G in order to give the gtf file but the output reported the chromosome coordinate. Why? What did I get... -
TopHat2 fusion-search : SeqAn error
Hi everyone,
I am using Tophat v2.1.1 with the option --fusion-search.
I downloaded the example and tried exactly the code in...Last edited by bibi; 04-20-2016, 11:28 PM. -
Low mapping rate of TSS-data (5'-seq)
Hi,
We have performed transcription start site sequencing (TSS, 5'-sequencing) using TAP treatment (tap+ and tap- of totalRNA) and Illumina... -
Adapter_and_kmer_trimming
Hi everyone,
I am using publicly available, 51 bp paired-end RNA seq data and I have some questions concerning the quality trimming of... -
Tophat/Bowtie
Hi, I am self learning tuxedo suite for RNA-seq analysis. I keep getting error messages and some how I can not go forward beyond tophat. I downloaded... -
TopHat2 command
Hello, I am not a bioinformatician I am more of a bench scientist. I am trying to align illumina bodymap 2.0 RNAseq files from ENA to the hg19 .fa file.... -
STAR vs tophat2 - mapping reads to long exons
Hi,
I have some RNA-Seq from the fruit fly, where we test the differential gene expression of several knock-outs and developmental stages.... -
TopHat -M/--prefilter-multihits; unmapped reads
hi!
i am confused when to use TopHat "-M/--prefilter-multihits and when not
"When mapping reads on the transcriptome,...
