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Is BED file generated by bametobed sorted ?

bedtools ngs bamtobed coverage sequencing written 4 months ago by pacman • 50 • updated 4 months ago by Alex Reynolds ♦ 27k

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How to interpret the outputs generated from bamtobed using BedTools?

bedtools bed bam bamtobed written 3.6 years ago by Louis Kok • 10 • updated 3.6 years ago by Sukhdeep Singh ♦ 9.6k

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Recent Replies

C: how to run mscore in bash? by genomax ♦ 62k
Use these for some inspiration : https://www.biostars.org/p/301755/ https://www.biostars.org/p/34...
C: Number of discovered genes in genome does not correspond with published annotati by genomax ♦ 62k
> claims to discover 53,065 coding genes, Are those total number of transcripts by any chance?
C: Blast wrong, RNA seq by genomax ♦ 62k
Are these segments similar to each other or different? If you have NGS data you should ideally be...
C: SRA and the relationship between biosamples, experiments and runs by JJ • 430
Thank you very much for your answer. However, I am still not getting it. Sorry ... I am trying to...
C: Finding a suitable Independent Variable for a Protein sequence homology analysis by natasha.sernova • 3.3k
See this Nar article: H1 histones: current perspectives and challenges Sean W. Harshman Nicolas...
C: how to run mscore in bash? by hektor102 • 0
OK! I explained in edit :)
A: Get mRNA sequence from UCSC genome browser using coordinates by piyushjo • 110
Instead of UCSC browser you should try Ensembl Biomart. You can get mRNA sequence of each transcr...
C: how to run mscore in bash? by ATpoint ♦ 13k
didn't work is the most uninformative error message in all of science ;-) Please avoid this a...
C: How to run the ViennaRNA package by cschu181 • 1.5k
Let's take a step back. The ViennaRNA package is used for RNA secondary structure prediction (gen...
C: How to get percent identity from bam file ? by Adrian Pelin • 2.2k
Sorry Pierre but I think the original question asked a read by read assessment of percent identit...
A: How to extract only sequences that contain a specific percentage of Cysteines ( by cpad0112 ♦ 11k
with [seqkit][1] and awk: $ seqkit fx2tab -B "C" test.txt | awk -v OFS="\n" '$3>=10 {prin...
C: samtools filter proper paired alignment by ATpoint ♦ 13k
Did you read the part about supplementary alignments?

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