Tag: bedGraph

Bedtools genomecov – Bam to bedgraph conversion 1 Dear all, I would like to convert sorted and indexed bam file (~20GB) to an bedgraph file and used the following command: bedtools genomecov -bg -split -strand – -ibam sorted.bam It’s been 3 days since I executed the command, still I couldn’t…

Perhaps try BEDOPS bam2bed and sort-bed to convert your BAM data to UCSC BED? $ bam2bed < foo.bam | sort-bed – | cut -f1-6 > foo.bed Then make a custom track from it, using the full, pack or squish display modes. If you zoom out far enough, you can get…

STAR- error 0 Hi. I’m trying using aligner STAR, with the follow scprit: /opt/STAR-2.7.9a/bin/Linux_x86_64/STAR –genomeDir /home/julia.nicoliello/genome_index –readFilesCommand zcat –readFilesIn /home/julia.nicoliello/fastq-files/Giselle_S13_L002_R1_001.fastq.gz /home/julia.nicoliello/fastq-files/Giselle_S13_L002_R2_001.fastq.gz –outFileNamePrefix /home/julia.nicoliello/resultado_star –outFilterType BySJout –outSAMunmapped Within –outSAMtype BAM SortedByCoordinate –outSAMattrIHstart 0 –outFilterIntronMotifs RemoveNoncanonical –runThreadN 20 –quantMode TranscriptomeSAM –outWigType bedGraph –outWigStrand Stranded But, I have error 109, with this message:…

Significance Proteins are the key drivers of neuronal synaptic function. The regulation of gene expression is important for the formation and modification of synapses throughout the lifespan. The complexity of dendrites and axons imposes unique challenges for protein supply at remote locations. The discovery of messenger RNAs (mRNAs) and ribosomes…

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

What you describe seems to be a difference in signal-to-noise ratio which is not uncommon. This is where more elaborate normalization methods such as TMM from edgeR or RLE from DESeq2 come into play. See the following links on why these methods are superior. The videos talk about RNA-seq but…

I’d like to use bedtools to create strand-specific per-base coverage profiles for my paired-end bam alignments of stranded RNA-seq data. Existing Biostars answers here and here suggest using bedtools genomecov with the -5 option to extract only coverage from the 5′ ends of fragments. These are the commands that I’ve…

Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark 0 Hello, previously, I was using Bismark with the ‘–comprehensive’ option to generate the individual bedgraph files from which we made the bigWigs. For one particular figure, my boss wants me to generate merged bdg files so that we…

Visulization of raw 4C-seq reads in UCSC 1 I’m trying to create bedGraph files to view raw and normalised reads from a 4C-seq experiment to view in UCSC for two biological replicates. Is there a simple way to do this? I’ve tried using bamCoverage and expected to get peaks for…

Merge regions in bedgraph file 1 I have a bedgraph file with the chromosome, start and end point, and the coverage: CM000994.3 10167710 10167711 95 CM000994.3 10167718 10167720 95 I want to merge regions that are close together. With a bed file I could use something like this: bedtools merge…

Using MACS2 parameters 0 Trying to reproduce a galaxy training in Linux CLI. I’ve come up with the following commands for the peak calling with MACS2. Am I on the right track? The galaxy parameters are- macs2 command can be- macs2 callpeak -t input_file.bed -n macs_output -g 50818468 –nomodel –shift…

Merge regions in bedtools genomecov/bedgraph file 0 I want to calculate the number of reads mapping to regions of the genome, and I want to group these reads into bins of say 1kb. I have used bedtools genomecov to generate a bedgraph file that shows the coverage of reads across…

STAR split reads into two strands 0 Hi all, I’m trying to find a way to split reads mapped with STAR into two separate bam-files, one for each strand. STAR is able to do that when creating bedgraph or bigwig outputs (–outWigType and –outWigStrand), however I can not find any…

Compare bedgraphs of two treatments after MACS2 callpeak . Output Files of MACS2 bdgdiff . Hello everyone, I have some bedgraph files from a ChIP- … Source link

callpeak: Main MACS2 Function to Call peaks from alignment results. bdgpeakcall: Call peaks from bedGraph output. bdgbroadcall: Call broad peaks … Source link

MACS2 bdgcmp for two bedgraph peak callingKeep it as 1.0 or default in most … bdgcmp Deduct noise by comparing two signal tracks in bedGraph. Source link

MACS2 bdgcmp for two bedgraph peak calling Mar 16, 2015 · I have the data in Bedgraph. MACS2 can use bedgraph as input for peak calling. Source link

bedGraph chrom.sizes myBigWig.bw (Note that the bedGraphToBigWig program DOES NOT accept a gzipped bedGraph input file.) Move the newly … Source link

Convert Sam To Bigwig Convert BAM into bigwig for chicken Hi, I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to- … Source link

It is too easy to make error report in the bedGraphToBigWig process. I want to save the time for the fresh people. The following procedure would be work well for majority situations.  1, bedGraph should be without header before sorting awk ‘NR!=1’ input.bedGraph > input.deheader.bedGraph 2, bedGraph should be sorted sort…