What Do The Columns Of "Junctions.Bed" File Mean?

Hi,

I have seen the junctions.bed file created everytime I run tophat. I tried reading through the manual, but I could not find a satisfactory explanation for all of the columns in this file.

Is there any resource where this description is available in detail.

bam tophat

• 5,193 views • link

updated 12.8 years ago by cpcantalapiedra

• written 12.8 years ago by Sameet •

1 answer

junctions.bed. A UCSC BED track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.

If you go to UCSC BED format http://genome.ucsc.edu/FAQ/FAQformat.html#format1

• 0 views • link

written 12.8 years ago by cpcantalapiedra

More posts like this

How to convert .bed file to .juncs file using Tophat?
written 9.7 years ago by heir_of_isildur88 •

Hi all, I am trying to convert the junctions.bed file to a new_list.juncs file in Tophat. In my Linux server, I tried inputting bed_to_juncs junctions.bed …
"deletions.bed" file of tophat2 output' s mean.
written 10.9 years ago by leenaehyeon •

I've alignment using Tophat2, and got ".bed"files, including deletions.bed, insertion.bed, junctions.bed and I opened the "deletions.bed" file. There are 4 columns ``` track name=deletions description="TopHat …
Doubts Regarding Calculation Of Fpkm Values By Cuffdiff?
written 12.7 years ago by Sameet •

Hi, Recently we sequenced a bunch of RNA Seq libraries. I wanted to compare the gene expression levels between all of them. So I used …
A Question About Samtools And Calculating Depth
written 13.3 years ago by Sameet •

I have some RNA-Seq data. I want to know if there is a way to use <code>samtools</code> to calculate strand-specific depth from the <code>accepted_hits.bam</code> file …
More Issues With Cufflinks, Tophat And Cummerbund: No New Transcripts Detected?
written 13.3 years ago by Sameet •

I am currently dealing with a number of RNA-Seq runs. We are using MiSeq for sequencing. We have one Wild Type and a number of …
Looking For Reasons Of Why The Results Of A Tophat Fusion Post Is Empty
written 13.4 years ago by KS

Hello Everyone, I ran tophat-2.7 on the example data with <code>--fusion-search</code> , it ran successfully and produced the following output files: <code>accepted hits.bam, deletions.bed, insertions.bed, …
What Kind Of Inputs Does Cuffdiff Take?
written 13.5 years ago by narges •

Hi, I have run tophat over the RNA-seq data and I got the output files : accepted_hits.bam, insertions.bed, junctions.bed, deletions.bed, unmapped.bam. Now to find …
Obtaining Junctions.Bed File From Aligners Such As Gsnap
written 13.7 years ago by Varun Gupta

Hi Everyone I am interested in getting the junctions.bed file similar to the one we get when we run tophat but with different aligners like …
Error With Samtools
written 14.1 years ago by Sameet •

I recently tried to use bowtie2 and <a href='http://samtools.sourceforge.net/'>samtools</a> to process some paired end data. I used bowtie2-build to index my reference genome, and used …
Junctions.Bed File Produced From Tophat
written 14.5 years ago by Varun Gupta

Hi everyone I am using Tophat for my analysis on RNA seq data After I ran Tophat on my reference geneome(which is basically for 80 …