Hi, All! I have a question about the usage of the bedtools fisher tool. I have posted elsewhere but have not received answers.
I am trying...
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BedTools Fisher Question
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Couting number of similar reads in sam file and output in bed file
Hi all,
Currently, after mapping, I got a sam file which contained approximately 30 million mapped reads. Then, by using bedtool bamtobed, I was... -
Unable to intersect BAM file with bedtools
Hi everyone, I'm trying to use bedtools intersect to check the number of mapped reads in target regions (in a .bed file) originated by targeted bisulfite... -
Question on reads mapping smallRNA-seq (100% feature coverage)
Hi all,
I have a fastq file containing reads from an Illumina NextSeq smallRNA sequencing, a fasta file representing the genome (it is composed... -
bedToBam gives empty output
Hi all,
I am trying to convert a .bed file which I made from data from an ancient genome tiling microarray into a .bam file. I am running... -
How to compare single-end vs paired-end RNA-seq data?
Hi all,
I’d like to compare RNA-seq data of WT (single-end RNA-seq) vs KO strain(paired-end RNA-seq), as follows:
wt 0hr... -
MACS2 output on Galaxy not readbale by BedTools on Galaxy
Hi!
I am getting the following error with Galaxy (need to get an answer specifically for Galaxy; without Galaxy I am not getting this error):... -
Can or should we perform feature counting with `bedtools intersect -c`?
I have the following BAM file and a annotation file.
What I want to do is to calculate reads count in
I can do it with the following three... -
bedtools - adding fields to bedpe files
Bedtools documentation states that one can add two extra fields to a bedpe file when using bamtobed. Does anyone know how to do that? I need to add the... -
weird compiling of bedtools
Hi all,
I am updating to the newest version of bedtools (v2.26). Upon compiling the application, I get a weird effect. Essentially, when I go and... -
bedtools makes ubuntu 14.04 slow
When I run bedtools 2.25.0 covereBed, the command below does run.
...Code:coverageBed -d -g custom.genome.txt -a targets.bed -b file.txt
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QTL overlap (bedtools)
Dear all, I am trying to compare some QTL regions with specific genome regions that I have, for it I am using bedtools.
I used before bedtools with...Last edited by clarissaboschi; 06-01-2016, 12:27 PM. -
Stats help, interpreting the output of bedtools fisher
Forgive me if this is trivial, I want to make sure I understand the output of bedtools fisher. I've used it to compare several sets of intervals in the... -
Chrom Sizes for Ensembl Reference
i want to convert BAM to BigWig for ensembl reference genome (Homo_sapiens.GRCh38.81.fa to be specific) using the following work flow.
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Need help understanding the method from this paper
I'm trying to somehow follow the method outlined in this paper for calling breakpoints after assembly and mapping to the reference (see Assembly and Validation)....
