Per Base Coverage
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.
View ArticleGetting The Average Coverage From The Coverage Counts At Each Depth.
Hi, I have read quite a few posts here about coverage already. But I still had a few questions. I have a BAM file I'm trying to find the coverage of it (typically like say 30X). So, I decided to use...
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 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...
View ArticleCalculating Exome Coverage
*// 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...
View ArticleHelp 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 ArticleSplit A Bam File Into Several Files Containing All The Alignments For X...
Hi everyone! I am struggling with annotating a very big .bam file that was mapped using TopHat. The run was a large number of reads : ~200M. The problem is that when I now try to Annotate each read...
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 ArticleReporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
I am trying to use bedtools to pull out the reads falling directly within a set of BED coordinates. While this command does it successfully:intersectBed -abam mybam.bam -b intervals.gff -wa -wb -f 1 |...
View ArticleProblem With Counting Mapped Reads
Hi, This is my very first experience analysing RNAseq data. My goal is to do differential analysis between two strains of a bacteria. So far, i managed to align and produce SAM and BAM files. I'm...
View Articlebedtools intersect - something wrong with chromosome numbers >= 10?
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...
View ArticleError In Bedtools Getfasta: Chromosome Not Found
Hi, I am triing to use BEDtools to get some sequences from genomic coordinates. But I am having an errors saying " WARNING. chromosome (chr12) was not found in the FASTA file. Skipping." for each read...
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 Can I Merge Intervals ?
Hello everybody, I should be grateful if you would kindly help me de fix my problem. I have a table like that :Chromosome start end info1 info2 chr01 1 100 15 35 chr01 150 300 15 39 chr01 299 750 16...
View ArticleHow To Rearrange Paired End Bam File?
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...
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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 ArticleGetting Unmapped Reads: Comparing Fastq To Bam
given a FASTQ file and a BAM file of aligned reads, is there an efficient way to get all FASTQ reads that are in the original FASTQ but not in the BAM? Perhaps using bedtools. i.e.:unmapped_script...
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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 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 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...
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