Hi everyone!
I’m currently analyzing NGS data and am looking for advice on the best approach to calculate gene coverage on a base-by-base...
16 results in 0.0021 seconds.
-
Base-by-Base Gene Coverage Analysis in .bam Files Using samtools
-
Having poor coverage depth using Pacbio hifi ccs reads for HDV viral Genome.
Hello everyone,
I'm currently working with PacBio HiFi CCS reads data for the HDV virus, and I've been using tools like pacbiominimap2 (PBMM2)... -
The R-square between coverage and short variants number
Hello, everyone
I've called variants with 3 kinds of short variants caller to decide which one to use for calling variants.
... -
Calculating depth of coverage for overlapping paired-reads
Hi all,
I have a question on calculating the overall depth of coverage for exome or targeted panel sequencing samples.
As a simple... -
Illumina Hiseq 3000 / enough coverage for RNAseq analysis
Dear all,
I want to sequence total RNA samples from Human on Hiseq 3000 for the first time. Do you have any idea how many samples per lane... -
Calculating coverage for regions with at least 1X for every nucleotide
Hi there, I have some WES samples been mapped.
Without using the manufacture interval BED file, I am wondering if there is any way to... -
WES - how deep do you sequence your germline control
Hello Seqers,
we currently do WES with a mean coverage of ~120x for tumor as well as the germline samples. Since we only use the germline... -
Amplicon sequencing coverage calculation
Hi,
Could anyone explain how the coverage is calculated in amplcon seq. Since a target is PCR amplified and sequenced and there is a lot of duplication... -
VCF file / relationship between QUAL and DP fields
Can someone explain to me if there is a relationship between QUAL en DP fields in a VCF file.
If I understand well, a high DP value (coverage)... -
1000 genomes and depth of coverage
Hi all,
I am interested in obtaining information regarding the depth of coverage for specific regions of the genome from the 1000 genomes... -
What precisly does the "cov" attribute in Cufflinks measure?
In Cufflinks analyses of RNA-Seq data, what exactly does the "cov" (coverage) attribute measure?
In the CuffLinks manual, it... -
Filtering in Picard HSMetrics?
I've been using HSMetrics for a while to get 2X/10X/20X/30X coverage, as well as average probe and target coverage.
I've noticed lately... -
Calculating percent covered per chromosome
Hi All,
I would like to calculate the percent of a chromosome covered at various depths. In other words, to answer how much of chrY was... -
RRBS acceptable coverage
Hi all,
I am new in RRBS. I want to use the gel-free protocol descripted in the article of Boyle et al. Genome biology 2012, 13. I want... -
Contig coverage from ALLPATHS-LG
Hi,
I have recently done my first de novo assembly with ALLPATHS-LG. I was wondering if it was possible to determine the coverage for each of the...
