Hi,
I’m working with some clinical exome sequencing data and I have a few questions.
I followed the GATK’s best practices...
20 results in 0.0023 seconds.
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hg19 vs hg38. Notable differences.
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LiftOver h19 to canFam3
Hi all,
I am trying to convert hg19 coordinates to canFam3 coordinates ( in *.bed format obviously) but liftOver does not seem to work... -
HISAT2 vs. TopHat2: Discrepancies between Hg19 & Hg38
Hello everyone,
I have around 150 RNA-Seq datasets created using the Lexogen SENSE mRNA-Seq Library Prep Kit for Illumina, as well as around... -
Homer makeTagDirectory error with hg19
I have installed hg19 for homer but when I try to make a tag directory:
makeTagDirectory my_tagDirectory -checkGC -genome hg19 -format... -
Genome hg19**not found in homer config
I want to use the Homer to do annotation.
After I input "annotatePeaks.pl 31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt" , it shows... -
HG19 Genome/Exome Visualisation
I want to visualise my Paired-End reads (.bam/.sam) files against the human HG19 genome. Does anyone know if their is a tool that is able to show the... -
BEAGLE errors: Allele not in marker file / Number of fields in .gprobs isn't %3
I'm trying to phase a specific genome against the 1000 genomes data.
What I've done so far:- fastq-dump --split-3: SRA -> FastQ
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BSGenome hg19 package - exclude scaffolds and contigs
Hi,
I am wondering if there is a way to exclude the scaffolds, contigs etc. from the "BSGenome.Hsapiens.UCSC.hg19" package without... -
How to convert to or get 1000 Genomes phase1 data mapped to hg18.
Hello.
I'm trying to annotate my variant data with 1000 genomes phase1 data.
(ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf)... -
Calculate mappability for an interval?
Hi all,
I downloaded the mappability file from here:
ftp://encodeftp.cse.ucsc.edu/pipelin...odeMapability/
then...Last edited by Vasilisa; 01-16-2013, 09:06 AM. -
Calculate mappability for an interval?
Hi all,
I downloaded the mappability file from here:
ftp://encodeftp.cse.ucsc.edu/pipelin...odeMapability/
...Last edited by Vasilisa; 01-16-2013, 07:10 AM. -
Converting Tophats bam output back to separate paired end read fastq files
Hi all,
I was wondering if anyone could offer me some advice on using paired end reads with Tophat, specifically with the output. I'm planning... -
Basic statistics from alignment using bwa
Hi everyone,
I have a couple of questions that I am sure most of you are already good at. I searched the forum but haven't seen similar... -
hg19 to Broad b37 coordinate conversion
Hi,
We'd like to convert hg19 coordinates to Broad's b37 reference coordinates. For example UCSC's "Known Genes" annotations can only... -
Convert hg19 to rCRS positions for chrM
Hi all,
I have a list of SNPs (vcf file) for chrM originally obtained using hg19 as a reference genome. I would like to convert the positions...
