bamtobed Posts

Latest

Open

RNA-Seq

ChIP-Seq

SNP

Assembly

Tutorials

Tools

Jobs

Forum

Planet

All »

Home

Welcome to Biostar! about • faq • rss

Community

Log In

Sign Up

Add New Post

Showing: bamtobed • reset

or Classic search

votes

answer

259

views

answer

Is BED file generated by bametobed sorted ?

bedtools ngs bamtobed coverage sequencing written 9 months ago by pacman • 50 • updated 9 months ago by Alex Reynolds ♦ 28k

vote

answer

2.8k

views

answer

How to interpret the outputs generated from bamtobed using BedTools?

bedtools bed bam bamtobed written 4.0 years ago by Louis Kok • 10 • updated 4.0 years ago by Sukhdeep Singh ♦ 9.8k

Recent Votes

Recent Locations • All »

France/Nantes/Institut du Thorax - INSERM UMR1087, 1 minute ago
United Kingdom, 2 minutes ago
United States, 3 minutes ago
Sweden, 12 minutes ago
Korea, 21 minutes ago

Recent Awards • All »

Autobiographer to Torrey Ah-Tye • 10
Autobiographer to Baylie_321 • 20
Scholar to Bioinfonext • 150
Scholar to evelyn • 30
Commentator to ATpoint ♦ 19k
Teacher to ATpoint ♦ 19k

Recent Replies

C: Is it possible to detect lncRNA in a de novo assembled genome? by Sishuo Wang • 170
Yes, if those transcripts are long enough and do not have any coding potential.
A: Kissplice2refgenome does not handle # in the very begining of GTF files by vincent.lacroix • 90
Dear Thibault, Sorry for answering so late to this post, but yes this issue was corrected a long...
C: Quantify expression from CAGE data by ATpoint ♦ 19k
You should state in which format you have the data. Fastq, Bam, count matrix...
C: rnaseqcomp for own data withoutref genes by ATpoint ♦ 19k
Not helping with your question but you better compare recent tools such as kallisto to salmon rat...
C: Biological replicates and depth seq by ATpoint ♦ 19k
Any idea why these two "groups" exist, is this maybe a strong batch effect? This cannot be all ba...
A: Kissplice2reftranscriptome error : IndexError by vincent.lacroix • 90
Dear user, This bug should now be solved with version 1.3.3 of k2rt available here: http://kissp...
A: VCF merge or concatenate? by harish • 200
Bcftools does this, but is much faster than vcftools. You have one sample, but the data is split...
C: basename: missing operand by Carambakaracho • 1.4k
Check `echo ${INPUT_FILE_ONE}`, if that's what you expected the pipe to sed is not needed and `.s...
C: Genomic coordinates from GENCODE annotation file by husensofteng • 110
although it is late, but I just wanted to point your attention to the genome build for the varian...
C: Regarding getting gene count tables for DeSeq from StringTie using prepDE.py by kousi31 • 0
Hi, Did you find an answer for this question?
C: List of sequences to gene symbol by catechize.2.learn • 80
Thank you @genomax.
C: Effect size in power analysis when dealing with Poisson based variant caller by CY • 370
I will have to give up detecting somatic variant with very low frequency (<1%) since matched n...

Content

Help

About
FAQ

Access

RSS
Stats
API

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Traffic: 730 users visited in the last hour