Help With Exception When Using Bedtools Coveragebed With Paired Alignment....
I use bwa mem to align paired reads to few hundreds of microbial contigs; then I sort the alignment, and trying to get a coverage using bedtools genomecov -ibam alignments.paired.sorted.bam -bg...
View Article"mask" values in a bedgraph
I am trying to plot average conservation in a list of genomic features, and so far managed to do it successfully using a combination of the phastCons bigwig files (hg19.100way.phastCons.bw) and...
View ArticleBedgraph Not Displayed In Igv
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 >...
View ArticleHow To Get Fasta Format Using Fastafrombed Or How To Turn Linearized Fasta To...
I extracted sequences with fastaFromBed and have no complains about the BEDTools which is really awesome thing.Otherwise extracted sequences look like this:>chr19:13985513-13985622...
View ArticleIntersectbed/Coveragebed -Split Purify Exon?
all.reads.bam file records mapped RNA-seq reads data, including:exon:exon junctionexon bodyintron bodyexon:intron junctionQ1: When calculating RPKM for given RefSeq gene including all the position...
View ArticleHow To Extract Scores From Bedgraph File Using Bed Tools
file1chr1 10 20 name 0 +file2chr1 12 14 2.5 chr1 14 15 0.5How could i extract average scores of file1 using file2, like below? I am trying to extract phastcons (file2) average scores of file1.chr1 10...
View ArticleHow To Combine Fpkm Values From Cufflinks With Contigs From De Novo Assembly...
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...
View ArticleBedtools subtract not dealing well with large datasets
I am using bedtools subtract with large datasets and it keeps crashing, giving the following error   terminate called after throwing an instance of 'std::bad_alloc'Is there a way to get over this...
View ArticleIs It Possible To Filter Only Bookend Reads From A Bed File?
I have a bed file with many fragments, some overlapping, some on their own and some adjacent to each other (book-ended) features.I know can group overlapping and book-ended features using bedtools...
View ArticleFiltering Bed Files By Using Bedops
hello every one,I have paired end illumina reads, R1.fastq and R2.fastq and I have mapped them as single-end reads by using bowtie2 default parameters, I performed further downstream analysis by using...
View ArticleMemory Efficient Bedtools Sort And Merge With Millions Of Entries?
I would like to know if there is a memory-efficent way of sorting and merging a large amount of bed files, each of them containing millions of entries, into a single bed file that merges the entries,...
View ArticleExtract rows from BED file on the base of text content in one column
Hi,I am a newbie with scripting so I can't find an easy solution to this question by myself and I'd like to ask for some help.I have a long list of BED files, and for each file I want to scan them row...
View ArticleReproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But...
Motivation The ENCODE data comes out, and luckily they provide both .bam file and .bigwig file. Thus, it occurs to me that I want to give a try to reproduce the data visualization with tool: BEDtools...
View ArticleCounting The Whole Insert Size From Paired-End Reads As Coverage
We have updated our workflows for per base sequence coverage to use genomeCoverageBed from BAM files. However for pair-end data it seems as though the regions between pair-end reads are not counted. To...
View ArticleCoveragebed, Depth/Breadth Of Coverage
I'm using coverageBed to calculate the depth and breadth of coverage, but I'm not sure I'm doing this right. I want to calculate the two values for each human chromosome. For example, I've created a...
View ArticleBedtools Intersectbed
Apologies if this is blatantly obvious!I would like to compare coordinates in setA with those of setB. The output should have the same number of coordinates as setA and tell me how many nucleotides of...
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Converting Bam To Bedgraph For Viewing On Ucsc?
I'm trying to go from a BAM file to a representation viewable in UCSC, ideally bedGraph. I am trying to use Bedtools's genomeCoverage like this: genomeCoverageBed -ibam accepted_hits.sorted.bam -bg...
View ArticlePicking Random Genomic Positions
I do have a set of TF binding coordinates and want to see if there is any significant overlap with an open chromatin annotation.Example of TF coord: chr1 19280 19298 chr1 245920 245938 chr2 97290 97308...
View ArticleFastafrombed Problem
hi, I try this tools from BedTools but it doesnt work!$ cat testgenome404.fa>chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ ./fastaFromBed -fi testgenome404.fa -bed...
View ArticleBedtools Genomecoveragebed Usage : How To Create A Genome File?
I am using BEDTOOLS and the following command to get the coverage file:$ ./genomeCoverageBed -ibam ~/GG_project/trim/ecoli.bam -g > ~/GG_project/trim/coveragewhere ecoli.bam is my sorted bam file,...
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