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alignment view and vcf disagree
I have a pacbio CCS fastq file that I have aligned to a small (5037 bp) reference which is part of a sequenced BAC clone. I have aligned this data with... -
IGV-Compatible FASTA Nomenclature to Indicate a Split Sequence?
Hi! New poster here, so please tell me if I should make any changes in post style or should have used a different subforum!
This is a x-post... -
In IGV 2.4.10 Squished view captured by Batch script, color of deletion looks white
I use IGV version 2.4.10. In Squished view, color of deletion sites is black. And when I use PrnScn key, color of deletion sites in the output image (png... -
Stranded library IGV
Hi all,
Could someone please explain the "color by first-in-pair" in IGV which was suggested by Jim Robinson in this post:
ht... -
IGV not creating genome
hello everybody
I am having trouble in creating a new genome file in IGV. The fasta file is not upolading. Have made a new index bai with samtools... -
IGV or IGB
Hi,
In the past I used to work with IGB, mainly for DNA-seq.
I started working in a new lab, and the genome browser they have been... -
Samtools how many reads were mapped as a pair
Hey, I am new to bioinformatics. I get stuck on the question How many reads were mapped as a pair.
I have created a .bam file that only contains... -
Visualize just non-synonymous variants in IGV
Hello,
I used snpeff to annotate a set of variants and I would like to only visualize where a particular type of variant (non-synonymous... -
General IGV question about pileup
In IGV what does a variant found only in white space denote. I don't think its real but trying to figure it out. For example, in the attached all the... -
Help with genes.gct file on IGV
Hello All!
I am using RNAseq data from a bacterium to identify genes that show differential expression. I used the genepattern platform... -
visualisation of RNAseq (kallisto to IGV)
Hello everyone,
as others, I am quite excited about pseudo alignment produced by kallisto in minutes instead of real alignment computed... -
Single-cell RNA-seq coverage track not corresponding to htseq-count output or IGV
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Chromosome sizes don't match
Hi,
I'm having a heck of a time finding the chromosome sizes for mm9 that match the mm9 Bowtie pre-built indexes on their website. I... -
TCGA RNAseq BAM Files
Hi
My PI is interested in acquiring BAM files of RNAseq of breast cancer/cancer tumor/cell lines. I know TCGA may have them, how can we... -
Data from servers Accessible on IGV
Hello, I have some questions about the server data accessible through IGV
1. When you upload files from the server "Body Map 2.0 (Illumina...
