I use bedtools's sortBed utility to sort BED files for various operations. It takes as input GFF files as well. However, when I feed it a GFF file as in:
sortBed -i myfile.gffit outputs it as GFF, not BED. Is there a way to make bedtools sort and then convert the result to BED? Many bedtools utilities have a -bed flag. Do I need to use a different subutility of bedtools to achieve this? thanks.
Hello, I have 2 bedfiles that share some common features let's call the first file A.bed (bigger file) and the second B.bed (smaller file). I would like to have a new bed file that includes everything in B.bed in the A.bed file. I don't need the intersect, I more like need the merge option I checked bedtools's manual... couldn't find an answer for merging 2 bedfiles. Can someone help?
Thanks in advance
Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.
I used paired-end sequence data for copy number variation study; and eventually get .txt files as output. I'm hoping to use Bedtools to compare my results with others.
Can I convert .txt files into .bed files? (I don't see option in Bedtools)
If Bedtools is not working, what software can I use for data comparison?
my lines of txt is just like:
deletion chr9:6169901-6173000 3100
deletion chr9:7657401-7658800 1400
deletion chr9:8847501-8848600 1100
deletion chr9:10010201-10011600 1400
deletion chr9:10126601-10127700 1100thx
edit: I converted the txt files into bedpe format, which looks like
chr21 18542801 18543500
chr21 18545701 18545900
chr21 19039901 19040600
chr21 19164301 19169400
chr21 19366001 19370200
chr21 19639601 19640300
chr21 20493701 20495700
chr21 20581401 20583000
chr21 20880901 20882700
chr21 21558601 21559700Then I started to compare two bedpe, looking for overlapping region, using the command like:
pairToPair -a 1.bedpe -b 2.bedpe > share.bedpeThen I see the errors:
It looks as though you have less than 6 columns. Are you sure your files are tab-delimited?MY bed file have only three columns, seems it requires 6....What's the problem here? thx
*// Edit to make the post more clear (Mapping done via Bowtie2). My problem is that when counting Exome Coverage via coverageBed gives different results than via genomeCoverageBed. So I'm not sure if I'm doing something wrong, or which of the 2 methods is correct.
1) My first step is to build an .bed file of my Illumina Paired-End reads, returning the positions that only fall in targeted exon regions. I'm doing that via intersectBed -a [data.bed] -b [illuminaexonregions.bed].
2) My next step is to calculate the coverage of my new datafile via coverageBed -a [newdata.bed] -b [illuminaexonregions.bed]. I calculated some statistics:
Number of exons 214126 with a total length of 45326818
Number of matched nucleotides 10993449.0
Nucleotides/Length*100 24.253740909 % Coverage.
3) The next step was to calculate the coverage of my new datafile via genomeCoverageBed -i [newdata.bed] -g [genome.txt] -d awk '$3>0 {print $1"\t"$2"\t"$3}'. I calculated some statistics:
Number of exons 214126 with a total length of 45326818
Number of matched nucleotides 10576907.0
Nucleotides/Length*100 23.3347661863 % Coverage.
Somehow there's a difference in matched nucleotides, which I can't explain. What am I doing wrong?
Hi, I am new and so facing problem. I was trying to make a bed graph file using bed tools genomecov command. The command was: bedtools genomecov -ibam filename.sorted.bam -g chromosome sizes.txt > O.bedgraph I got a bedgraph file which is much smaller in size. It is 500kb instead of ~6Mb. And when I load that 500kb file into IGV, I see nothing. Please help me out.
Hi. I have a folder full of .fa files, and a .gff. The gff file contains information about which loci look like they code for RNA sequences. The .fa contain the DNA sequences for a set of human chromosomes. I want to get all the sequences which code for RNA, as defined by the gff file, out of the DNA in the fasta files. I also have a file telling me which RNA types have higher priority (lincRNA is higher priority than miRNA for example), this tells me which are more important and how I should decided between RNAs for overlapping reads in the gff.
I have been trying to code my own little program in F# that will read these files and give me each RNA read defined in the gff, and its corresponding DNA. However I am a bit confused about how it works. Do the start and end of each feature in the gff file define a character in the corresponding .fa file? Are they 1 or 0 indexed? Does it matter what strand they are ('+' or '-') for my purposes?
Ultimately my goal is to get a bunch of RNAs with their corresponding types (miRNA, lincRNA, snRNA... etc) to do some computations on.
My question is this: what is the easiest way to get it out of the data I have?
The data I am using is freely available here: http://wanglab.pcbi.upenn.edu/coral/ under the heading "Annotation packages" if anyone is interested or needs specifics.
Thank you!
Hi,
I've downloaded the recent Cygwin version 1.7.24 and an trying to run bedTools but I get an empty file as my output. When I run the same commandline and files on a colleagues computer also through Cygwin I get a file containing the overlaps I seek. is the new Cygwin not compatable with BedTools? I've put the command line we used below:
./intersectbed -a Gene_body.bed -b EdgeR1.bed -wao > yyy.tempAny help would be appreciated.
genomeCoverageBed for my analysis. And I used the following command:genomeCoverageBed -ibam file.bam -g ~/refs/human_g1k_v37.fasta > coverage.txt
As many are aware, the output of the file looks something like this:
genome 0 26849578 100286070 0.26773
genome 1 30938928 100286070 0.308507
genome 2 21764479 100286070 0.217024
genome 3 11775917 100286070 0.117423
genome 4 5346208 100286070 0.0533096
genome 5 2135366 100286070 0.0212927
genome 6 785983 100286070 0.00783741
genome 7 281282 100286070 0.0028048
genome 8 106971 100286070 0.00106666
genome 9 47419 100286070 0.000472837
genome 10 27403 100286070 0.000273248
To find the coverage, I multiplied col2 (depth) with col3 (number of bases in genome with that depth) and then summed the entire column. Then, I divided it by genome length to get the coverage. In this case, col2 * col3 is:0
30938928
43528958
35327751
21384832
10676830
4715898
1968974
855768
426771
274030
And the sum is: 150098740. Since the genome length is 1002860 ...
Hi,
I am trying to extract the coverage and the average quality score for each position of a reference assembly in bam/sam format. I have managed to get the coverage using BEDtools
genomeCoverageBed -ibam mybamfile.bam -g my_genome -d > my_coverage.txtbut am at a loss on how to get some measure of the quality of the base calls at each position. I was thinking that I could use the bcftools to get a variant call formatted file
samtools mpileup -uf ref.fa mybamfile.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcfbut this only provides the sites for which there are SNPs. Any advice greatly appreciated.
Joseph
Hi,
I have question about bigwigsummary tools ,
I have my start and end positions and my bigwig file but I want to check whole genome instead of chromosome by chromosome Is there any option to use this tool in that way ?
I know that for each chromosome I have to use :
bigWigSummary -type=X bigwigfile chrN start end datapointsI want to check from chr1 to chrX.
Thanks in Advance.
With bedtools you can make genomic windows from a genome file or a bed file
input.bed
chr1 1000000 1500000
chr3 500000 900000[prompt]$ bedtools makewindows -b input.bed -w 250000
chr1 1000000 1250000
chr1 1250000 1500000
chr3 500000 750000
chr3 750000 900000Does the bedops suite provide a similar way to create genomic windows?
I'd like to count the number of unique genes in a gff file falling within a list of genomic regions. With bedtools I can count the number of regions within the gff which is almost what I want, but not quite.
bedtools intersect -a regions.bed -b my.gff -cUPDATE:
I should have made my question a bit more specific. I have a modified ensemble style gtf file (not a gff) that has unique transcript IDs. This means that simply selecting unique fields in the 9th column of the gtf file actually counts transcript IDs.
To circumvent this problem I first truncated the gtf file:
cat my.gff | sed -e 's/;.*//' > delete.me.gtfThen I ran the bedtools map command:
bedtools map -a regions.bed -b delete.me.gtf -c 9 -o count_distinct > counts.genes_in_windows.bedI almost forgot to delete the intermediate file:
rm delete.me.gtfThere is probably a way to make this a oneliner, without the intermediate file, but I have a dissertation to write!
I am using BEDTOOLS and the following command to get the coverage file:
$ ./genomeCoverageBed -ibam ~/GG_project/trim/ecoli.bam -g
where ecoli.bam is my sorted bam file, and coverage is my output file
From where do I get the genome file? How do I create a genome file?? Specifically I would need a ecoli.genome file.
I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks or DEXSeq,
Lets say that my exons are named 1,2 and 3, and I want to know in how many samples I have a splicing event of the number two, so i was looking in the threads and I found that using coverageBed with my bed file of the three exons I could get some kind of idea per bam file
coverageBed -split -abam my_alignment -b exons_to.bedAm I correct?
I was also thinking of getting the reads mapped in flanking end positions of read 1 and start of read 3 with samtools
What do you think about it? Any idea will be kindly appreciated
Thanks in advance!
How can I use the closestBed from bedtools to find the closest locations between two bed files. The important bit here is that i want them to be upstream and in correct oriantation.
When I use the -s option, it does not report anything (everything is -1).
Then I checked the -D a option. It is returning some results but not sure if it is the right thing.
The other thing to mention is that my genes bed file (lets call is gene.bed) is organized as
chr1 123 234 +
chr1 456 789 -rather than end position being smaller to indicate the negative strand.
Whereas my repeats.bed file are organized as
chr1 239 456
chr3 456 987Does bedtools get confused with this?
Which options should i use if i want to find the distance to nearest repeat that is upstream and in the correct orientation?
#-t 4 is for using 4 threads/cores
bwa aln -t 4 ./hg19.fasta ./s1_1.fastq > ./s1_1.sai
bwa aln -t 4 ./hg19.fasta ./s1_2.fastq > ./s1_2.sai
bwa sampe ./hg19.fasta ./s1_1.sai ./s1_2.sai ./s1_1.fastq ./s1_2.fastq > s1.sam
Supposed we wish to compress sam to bam, sort, remove duplicates, and create a bed file.samtools view -Shu s1.sam > s1.bam
samtools sort s1.bam s1_sorted
samtools rmdup -s s1_sorted.bam s1_sorted_nodup.bam
bamToBed -i s1_sorted_nodup.bam > s1_sorted_nodup.bed
This workflow above creates many files that are only used once (such as s1.bam) and we can use the unix pipe utility to reduce the number intermediate files created. The pipe function is the character | and what it does is ta ...
I have used the Bedtools command intersectBed to check the overlap between two bed files. A is my INDEL file and B is my Reference file. But it is producing an empty output file. I thought the problem was that the file B is much larger than file A. But I tried changing the file order and it is still not creating any output.
Here is the reference B file (larger):
gff_seqname 0 1395 gene 0 +
gff_seqname 0 1395 exon 0 +
gff_seqname 1397 2498 gene 0 +
gff_seqname 1397 2498 exon 0 +
gff_seqname 2524 3619 gene 0 +Here is my A file with just 51 INDELS:
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 174708 174713 -GCCGG:2/6
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1078686 1078686 +A:105/112
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1229123 1229125 -CT:800/870
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1234830 1234830 +AT:134/134
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1234833 1234834 -A:134/134here is my command:
intersectBed -a SOD_pal_BWA_GMM.PE.sorted.bam.sorted_cleaned_GMM.bam.sorted.hr.bam.raw.bed -b sodalis_galaxy.bed -wa -wb >test13.bed