Hi all,
Does anyone know where I would be able to get an annotated splice junction file that I could use with STAR? I've been searching for one,...
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Annotated junctions file for STAR
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Disparate numbers in IGV sashimi plot and junctions.bed
I trying to detect widespread splicing defects and amongst other things I ran tophat to find new splice junctions on my libraries (PE, 100 bases):... -
Tophat result: how to get the number for novel junctions
hi,
tophat can output a file junctions.bed including the splicing sites for junction reads.
Can I get novel splicing sites that... -
Tophat: generate junctions.bed file from BAM file
Dear all,
I have previously mapped RNA-seq samples to the human genome using Tophat 2.0.6. This generated an "accepted_hits.bam" result... -
junctions usage
Dear all,
I would like to know if there is a tool out there that can handle the junctions file coming out from Cufflinks and treat them... -
How to make sense of Tophat's output file 'junctions.bed'
This is an excerpt from junctions.bed, Tophat's output file generated using paired-end reads. Can somebody suggest how to make sense of the two bed blocks?... -
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... -
Obtaining Junctions from a SAM file...
Hi all. I was wondering if anyone knew of an easy way to obtain a list of junctions from a SAM file produced by Tophat. Unfortunately I do not have the... -
Running Tophat with the GFF option
Hello,
I am running Tophat with the --GFF option, where I supply it with the GFF of all the genes in my genome so that it can use those...
