10 results in 0.0031 seconds.
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Tophat using --no-novel-juncs
I would like to align my reads to the annotated human transcriptome. One idea would be to use Tophat with the -G option supplying refFlat.gtf from UCSC... -
Tophat paired end alignment.
Dear forum,
I have RNASeq SOLID data that is paired end. I want to use Tophat to perform the alignment. Does anyone out there know how... -
Problem using TopHat with SOLiD SE-reads
My first post to this forum... So please stay with me if I make some mistakes.
We did a SOLiD-run on HEK-293T cells transfected with a... -
Acceptable Sp/Sn output from cufflinks and problems with Homo_sapiens.GRCh37.60.gtf
Hi there,
I was wondering what levels of Sp/Sn people are seeing from Cufflinks output, and what you would consider as acceptable.
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multiple FPKM problem for single gene in gene_exp.diff after running cuffdiff
I ran tophat (1.1.0) without a mouse gtf file. Run cufflinks (0.9.1) without a mouse gtf file. Then run cuffcompare with a mouse gtf file and two gtf... -
help to create fastq file with non-aligned reads
Hi everyone,
So far I have been reading posts only, and it has been really helpful.
I am using TopHat to align Illumina sequences... -
Bowtie Index Files
Hi, everyone
I am a little confused about bowtie index files.
I am treating Arabidopsis and Oryza RNA-seq data.... -
TopHat err = -9
I am trying to run my RNA-seq data in TopHat and I keep getting the below error. I have tried the latest 1.1.0 version and it gave me the same error.... -
Abberant junctions by tophat
I have tried to align my paired end RNA-Seq reads to the genome using Tophat. I ran a sample dataset from the SRA (SR018268_1 and _2) and the data looked... -
tophat -r parameter
Does anyone have advice on what to use for the tophat -r parameter (mate inner distance)?
For example, if the lab cuts a ~200 fragment...
