Open Question:
Has anyone identified interesting sequence data from the sub nucleosomal size range, smaller than 150 bp.
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15 results in 0.0029 seconds.
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Sub Nucleosomal open chromatin regions
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Whole Genome from BAM File
Hello, Im a new to bioinformatics.
I have a whole genome of human in BAM file ~80 Gb. It is already aligned to B19.
can I get... -
Use Bowtie Index to get sequences using locations
We have the fasta files (obviously) for the hg19 genome, we used them to create a big Bowtie index.
I was hoping not to have to keep the... -
DNA strands coding in fasta file
Hi,
my question is:
how two strands of a DNA molecule are coded in a chromosome file in fasta format. Are each line coded... -
DNA in a chromose
Hi,
I am using the GRCh37 assembly on NCBI website. My question is:
which parts of each chromosome in chr*.fa file is for DNA and... -
Sort bed file by chr order and not lexicographically
I've been trying to sort a bed file with bedtools and bedops.
Both seem to sort the bed file lexicographically.
That means if... -
Plotting per chromosome coverage for BAM files
Hi,
I wish to plot coverage profiles for each of the chromosomes from my BAM files which I obtained after aligning exome sequencing data... -
How to fetch sequence from chromosome coordinates
Hi all
I have chromosome coordinates (e.g. 5233922 to 5235189 of chr18). how can I get the sequence corresponding to this region ?
Like... -
Paired Reads Mapping Across Chromosomes
Hello all,
I have some Illumina HiSeq paired end whole genome human data that has 2 - 3% of paired end reads where the two ends are mapping... -
Split up a Bam file with chrom-bed
I saw a couple posts, not specifically here but elsewhere that asked how one could divide a "bam" file into certain chunks or into its individual... -
Identifying chromosomal gene pairs
I have identified, via RNAseq, a number of differentially expressed genes located on the X chromosome. I would like to identify the pairs on the Y chromosome... -
Paired-end reads mapping to different chromosomes...
Hi there,
I've been stumbling through some Illumina HiSeq data for a while, and while I've managed to answer some of the questions we wanted... -
eland codes for unmapped reads?
Hi,
I'm analyzing some Illumina data (HiSeq) using Bioconductor and am curious to look a little bit more at the unmapped reads.
... -
Handling alignments spanning chromosomes boundaries in BWA
Hi All,
When BWA aligns a read that spans over two chromosomes, it sets the flag as "unmapped" but leaves mapping quality (MAPQ)... -
Library prep using chromosome sorted DNA
Does anyone have any experience with library preparation of chromosome sorted DNA? The main issue is that we are starting with only 120ng of material....
