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Profile Coverage Of Rnaseq Samples?
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...
View ArticleGet The Idea Of Splicing From Reads Mapped In Rna-Seq
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...
View ArticleSimple Redirection, I/O Problem With Bedtools
Hi Guys, Just a quick question. Its more of a Bash question rather than Bioinformatics, with Bedtools in question.I mostly pipe the bedtools I/O. Here's a general scenario :sed 1d fileA.bed |...
View ArticleBedtools To Compare A Vcf File From Samtools Mpileup With Dbsnp?
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...
View ArticleConverting Gff To Bed With Bedtools?
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...
View ArticleCorrelation Of Fpkm And Length Normalized Transcript Mapped Read Count
Hello, in the process of estimating expression for a 16 human tissue dataset ("Human Body Map 2.0 GSE30611") I used different methods to estimate the expression of the genes. After mapping against hg19...
View ArticleCounting Number Of Bam Reads Directly Within Set Of Intervals With Bedtools
how can I count the number of BAM reads falling directly within a set of intervals, given in a GFF format? Note that I do not want reads overlapping the intervals, but ones that fall directly within...
View ArticleHow To Use Bedtools To Extract Promoters From A Mouse Bed File
Hello, I would like to know how to use Bedtools to extract promoter sequences (as FASTAs) from the mouse genome (mm9) starting from a BED file.
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 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 ArticleUsing Gnu Parallel For Bedtools
I am trying to run gnu:parallel on bedtools multicov function where the original command is bedtools multicov -bams bam1 bam2 bam3.. -bed anon.bed > Q1_Counst.bedI would like to implement the above...
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 ArticleGetting Rna Sequences From Gff And Fa Files
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...
View ArticleHow To Get Annotation For Bed File From Another Bed File
Hello All,I have a bed file (with Chr, Start, End, Name, Score and Strand) Chr1 5678 5680 NA 7 + Chr1 700 800 NA 8 - Chr1 900 1200 NA 10 -and would like to know, how can I get the annotation for the...
View ArticleConvert Bamtobed Score
Hey,just a short question....is there a possibility to set the score in the bed file to "1" an not to the the alignment score?? arguments -tag and -ed only use BAM alignment tags... ?!? :/Cheers!
View ArticleBedtools Compare Multiple Bed Files?
I've been dealing with comparison between two bed files using intersectBed -a -b command. I'm just wondering, is there any commands in Bedtools which can help us compare multiple bed files? Say, I have...
View ArticleN Closest Genes To A Given Location
Hi,This is basically an extension of the following question already asked in biostar (http://biostars.org/post/show/53561/python-finding-gene-closest-to-a-given-location/).Let us say I have a list of...
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Extract Only Paired-End Reads That Map A Specific Interval
Hi,Is it possible to extract paired-end reads that map to a specific interval ( from a bam file ). I tried with intersectBed :intersectBed -abam align.bam -b interval.gff3 -wa > result.bamhere's the...
View ArticleGenomecoveragebed - Bedtool For Reporting Per Base Genome Coverage
Hi Everyone I would nedd some help on genomeCoverageBed tool. This tools when used for finding per base genome coverage uses an option -d. I am actually interested in finding read counts for each base...
View ArticleChanging Column Order In Bed File
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?
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