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.
Hi,
I am trying to use bedtools windows. It has been explained in the manual of the bedtools but I am still bit confused and thought a confirmation would be good. And I have no biological background.
I have divided my bedfile into two, based on the strand information(For example, posStrand.bed and negStrand.bed).
I would like to screen overlaps of LINEs within 5000bp upstream of my postStrand.bed file.
Hello,
I have one big vcf file which is genereated by samtools mpileup by comparing 6 cell lines to see whether there are SNP differences between them.
I would like to use bedtools for intersecting. How can I do it? do you have some scripts for that.
Thanks
I want to run subtract command in java, could somebody tell me how to use.
Thank you very much.
Here is my data with A, B, C and D columns in my bed file.
A. B. C. D.
Chr 1. 1. 12. +
Chr 2. 24. 56. +How can I move my D column to position 1 where the Column A right now?
*// 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?
Say I am working on a server with a shared file system and 4 quad core nodes (I/O is not an issue, 16 cores total). I want to run coverageBed across 20 files. Currently I have a shell script that would do this sequentially. It is possible to just background the command so they run in parallel but I am not sure how to block in BASH. (next step requires counting between the files) Assuming I/O is not a bottleneck, what are ways of leveraging the advantage of multiple nodes/cores when running bedtools (or any other sequential commands for that matter).
From my rudimentary understanding of parallel programming the concept I am trying to get at is how do you 'block' so that that the next command after coverageBed will not be executed until all coverageBed runs are done.
I was thinking of wrapping the shell commands in a python script and having queue of coverageBed commands and a function to feed commands 4 at a time (since quad cores) and the function would only return when queue is empty. Is there a better way of doing this?
Hi!
I have an alignment (.bam) of reads to mm9 genome. I sorted it with samtools sort, so that later I can use -sorted key with bedtools. I also created a .bed-file with regions of interest, in which I want to count number of reads, that mapped to them. I tried this: converted .bam to .bed with bedtools bamtobed, and then intersected them counting number of hits (bedtools intersect -a regions_of_interest.bed -b alignment_sorted.bed -c -sorted > Neg2H_counts.bedgraph). The problem is, it looks fine for all chromosomes with numbers from 0 to 9 (and X), but all counts for all regions of interest of chromosomes with higher number (chr10, chr11, etc) are 0. There is no biological reason for that, in fact the highest signal should be on chr11. What could be wrong here? I am fairly new to all these tools.
UPDATE
I tried to do the same intersection with bedmap and the result is identical... So there probably is something wrong with my files - what could it be?
I also tried sorting the alignment-derived bed-file in the same way, as I did with the files with regions of interest and it doesn't help.
1 exm2253575 0 881627 G A
1 exm269 0 881918 A G
1 exm340 0 888659 T C
1 exm348 0 889238 A G
1 exm2264981 0 894573 G A
1 exm773 0 909238 G C
1 exm782 0 909309 C T
1 exm912 0 949608 A G
1 exm991 0 977028 T G
1 exm1024 0 978762 A G
And I have all of the SNPs in dbSNP 138 downloaded as a large VCF file:
#CHROM POS ID REF ALT QUAL FILTER INFO
1 10019 rs376643643 TA T . . RS=376643643;RSPOS=10020;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000020001000002000200;WGT=1;VC=DIV;R5;OTHERKG
1 10054 rs373328635 CAA C,CA . . RS=373328635;RSPOS=10055;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000020001000002000210;WGT=1;VC=DIV;R5;OTHERKG;NOC
1 10109 rs376007522 A T . . RS=376007522;RSPOS=10109;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000020001000002000100;WGT=1;VC=SNV;R5;OTHERKG
1 10139 rs368469931 A T . . RS=368469931;RSPOS=10139;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000020001000002000100;WGT=1;VC=SNV;R5;OTHERKG
1 10144 rs144773400 TA T . . RS=1447734 ...
I have three bed files with chrNo, start, end position and type. I need to compare each chrNo, start and end position of one file with 2 other files and write the common one in a new file. Can any one suggest how can I do this efficiently? I wrote the simple perl script, but as the file is huge, it is taking a lot of time, thus is not feasible. Thanks in advance
Example files:
file1.bed:
1 20 30
1 100 120
1 200 300
file2.bed:
1 2 5
1 25 34
1 200 300
file3.bed:
1 30 33
1 200 300
1 500 600
common.bed
1 30 34 --> coordinates with overlapping 5bp is considered as same but outermost coordinates of the 3 is taken in common file
1 200 300
For example, we now have a bed file:
chr1 23455 45678
chr1 23446 45663
chr1 23449 45669
chr1 30000 31000Is there anyway to group the first three lines, while leaving the last line alone? I know Bedtools have mergeBed function, merging those overlapping span, which, however will include the last line.
This may sound a pure computational question; but I'm just curious if we have available tools already to tackle such questions
thx
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!
Hi all,
I have a quick question:
How can I visualize aligned paired-end reads from RNAseq datasets in UCSC browser?
I already mapped the reads and assembled the transcripts with Tophat/Cufflinks but I'm not sure how to proceed to visualize the mappings
After sorting the BAM files and fixing the mate pairs, I tried to compute the coverage using the following commands:
genomeCoverageBed -bg -split -ibam F.T0.rep2-accepted_hits-fS.bam -g ~/conversion_util/chrom.hg19.sizes > F.T0.rep2-accepted_hits-fS.bg
bedGraphToBigWig F.T0.rep2-accepted_hits-fS.bg ~/conversion_util/chrom.hg19.sizes F.T0.rep2-accepted_hits-fS.bwBut I was not able to visualize properly the mappings. Here I paste a screenshot of how it looks like:
Do you know where is the mistake?
Thanks!
genomeCoverageBed -bg -ibam sample1.bam > sample1.bedgraph
genomeCoverageBed -bg -ibam sample2.bam > sample2.bedgraph
unionBedGraphs -header -i sample1.bedgraph sample2. ...
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
Hi all,
I am working on RNA-seq data analysis. I've finished running Tophat and Cufflinks to get FPKM values for each read from Illumina pair-end sequence. Also, parallely I've run Velvet to get contig sequences through de novo assembly and Gmap to see if the assembled sequences map to reference genome (this reference genome is not complete for now, but somewhat useful). Now, I am trying to combine all information so I can have sequence information for a contig and FPKM value for the corresponding to the contig. Some suggested I can convert Cufflink and Gmap outputs to bedfiles and then use IntersectBed to see if there's any overlap. However, I am not sure how I can have every information saved in the output from Bedtools. IntersectBed default seems to provide me overlapped region with 'A' file as a template, so I couldn't see any information from 'B' file. Is there any solution for me?? Please let me know. I would appreciate for your suggestion!
chr start end gene number_of_repeats
chr1 100 200 gene1 70
chr1 190 240 gene1 40
chr1 250 400 gene1 100
chr2 500 600 gene2 150
if i sort and merge them i will get
chr1 100 240 gene1 90
chr1 250 400 gene1 100
chr2 500 600 gene2 150
So gene1 will have 190 (90 + 100) and gene 2 will have 150 number of repeats.
Or
b) shall I count the number of repeats which for each short sequence without any merging? ...
Hello all,
I have a paired end bam file and I want to use bedtools for them. After merging, the paired end read alignments are not lying next to each other. It is making problems in the bedtools process. Is there any tool available to rearrange the paired end read alignments in bam file?
Thanks, Deeps