Hi,
I have been aligning RNAseq data using tophat-fusion for downstream analysis of circularRNA using CIRCexplorer2 (requires tophat-fusion...
22 results in 0.0030 seconds.
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Tophat-fusion: Joining segment hits - FAILED
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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... -
RNA-Seq Data Analysis Workshop
RNA-Seq Data Analysis Workshop
Quality Control, Read Mapping, Visualization and Downstream Analyses
When?
September 23 -... -
BBmap generates Bam files with duplications in sequence sequence names
After running BBmap with the command like this:
...Code:java -ea -Xmx30g align2.BBMap build=1 overwrite=true fastareadlen=500 -Xmx30g in=8601_RG15-S1_IndexD706-D508_GAATTCGT+GTACTGAC_L007_R1_001.fastq.gz
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HiSAT2 RNAseq alignment low + stranded data predicted to be unstranded
Hi all,
I have been receiving some confusing output with an RNA-seq dataset that I am trying to ultimately determine differential expression... -
Align unmapped reads to virus genomes
Hello,
I am trying to determine how much of the unmapped reads from a transcriptome study align to viruses. My procedure so far has been...Last edited by SuzuBell; 10-23-2018, 05:45 PM. -
Htseq_processing double number of aligned reads
Hi All,
I am trying to generate count data from the bam files using Htseq. Our data was produced using Illumina stranded library and sequenced... -
Mapping using STAR and Bowtie
Hi all,
I want to perform an alignment of short reads against a reference genome (human genome from Ensembl). For that I've used STAR,... -
Hisat2 index with splice sites
Hello,
I would like to detect lncRNAs from RNA-seq data. Initially, I'm using Hisat2 for aligning the samples. For this I downloaded the... -
Too much "no feature" counts??
Hello,
I’m having some issues analysing RNASeq data on Chipster. I have single-end rna samples (brain) sequenced on a illumina NextSeq platform... -
STAR alignment - splice acceptor site vs mismatch
This is more a question about how STAR works. In figure 1 of the paper (here), the aligner can either look for a splice acceptor site or extend beyond... -
Fastx and Soapdenovo trans
Hello,
I have filtered my illumina pair-end reads (Forward lib-24 million reads, Reverse Lib 24 million) using FASTX_Quality_Filter by... -
Looking for advice on generating a transcriptome from mapped .bam or .sam files
Hello all. I'm starting off here with something fairly complex, I guess.
I'm looking for some advice because I'm starting a new project... -
Total RNAseq multiple mapping issue
We are running paired-end total RNA (using blood) on HiSeq and after adapter and quality trimming (Q>30), we use tophat2 for alignment. We are getting... -
Hello and Alingers for Transcriptome analysis?
Dear All,
Just wanted to say a big Hello and thanks to the community which has served its purpose well for so long. If it hadn't been for...
