54 results in 0.0026 seconds.
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Using IGV to View Alignments
Hello. I have some Bam files of illumina RNA-seq data aligned to the human genome that I would like to upload into the Broad's Integrative Genome Viewer.... -
RNA-Seq strandedness inconsistency
Hi,
Let me start of by saying that I am thoroughly confused and I hope someone can help me make sense of my data.
I have...Last edited by Anomilie; 11-20-2015, 01:41 AM. -
vcf from bam file
Hi,
I am trying to create a vcf from a bam file using samtools and bcftools
like that:
...Code:samtools mpileup -ugf ~/genomes/Mus_musculus/GRCm38.p2/mm_ref_GRCm38.p2.fa
Last edited by frymor; 06-25-2015, 06:56 AM. -
IGV colors entire BAM file as inversions
I'm using the Integrative Genomics Viewer (IGV) to view the alignments achieved from TopHat.
I have four samples (and thus four BAM files).... -
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how can I find a read in IGV?
Hi,
If I know the Read ID, how can i find it in integrated Genomic Viewer?
thanks! -
What does IGV track color alignments by strand when using non-stranded RNA-seq?
I'm currently working on a RNA-seq dataset that isn't stranded, but when I load the bam files into IGV... and click on the "color alignments by strand",... -
Manual Quality Control for Variant Calls
Hello all SEQers,
I am trying to find some documentation or leads on strategies for the manual quality control of variants that have been... -
Trying to check plasmid alignment
I have sequenced 2 samples (paired end). First sample is called Plas1 and second sample is called Micro_plas. I am interested in knowing whether Plas1... -
Identifying a good SNP on IGV
I start working with IGV, but I have some doubts in how to identify a good SPN in this program. First I download the new Soybean Genome on Phytozome (Gmax_275_v2.0.fa... -
GSNAP output to IGV
I aligned Illumina reads to the zebrafish v9 reference genome using GSNAP. I had to build a new genome database in GSNAP/GMAP from individual fastA files... -
Easy way to screenshot whole region from IGV?
Dear troops,
I use IGV to present mapping of my reads to a genome successfully.
Now, I want to capture the picture for my paper.... -
Visualize variants annotated with ANNOVAR
Hey all,
I'm developing a pipeline for NGS data analysis. I'm pretty much ok with the steps up to variant calling (I'm using GATK for that)... -
Making nice image of chr1 coverage track in IGV
Can anyone help me make this kind of image?
I have calculated the coverage track and visualised (as log values) compared to chr1 in IGV.... -
SAMtool merge/cat problem
Hi guys,
I d like to cat or merge 2 BAMs file. My problem is that I try to cat the two BAMs but when I ve used IGV to see the result the...
