54 results in 0.0026 seconds.
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IGV displays ">chr1 " as part of genome sequence
I was trying to figure out why all my chr1 alignments looked like they were full of mismatches in IGV, and then I noticed they were all off by 6 bp. I... -
How to add Arabidopsis T-DNA lines as tracks on IGV
Hi,
We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion... -
Significance of Pindel's "AD" and finding SVs in IGV
Hi All,
I am running pindel on some nextgen data for exploring ins, del, rpl, tandem:dup, etc. I have two questions:
1. I can...Last edited by opulcy97; 06-27-2013, 02:32 AM. -
IGV: empty tracks?
I am trying to load some .bam files into Integrated Genome Viewer. However, even when I zoom in to a particular gene that I've found to be differentially... -
Exporting data from .tdf files through IGV
Hello All,
I have multiple .tdf files that can be easily imported into IGV for viewing. My goal is to get the corresponding value (signal... -
Errors loading particular vcf files into IGV but not others
Hi,
(would've posted this in the google group but it's not letting me for some reason, so I thought I'd try SEQanswers instead)
... -
IGV reading .bam
Hi all,
I'm trying to open .bam file in IGV but I keep getting "sorted.bam does not contain any sequence names which match the current genome"... -
igv error with thophat2
Hi everybody,
I am running the tophat2 command like that:
...Code:tophat2 -p 4 -r 500 -o OUT_DIR chromosome.MT.fa R1.fastq
Last edited by frymor; 09-24-2012, 05:08 AM. Reason: new information. I ran the same tophat command with the MT genome w.o. the additional 500 bases and it works fine on igv -
How should a strand-specific experiment look like in IGV?
I have a paired-end, strand-specific dataset and used Trinity to assemble the contigs. I then mapped the reads back to the contigs to calculate transcript... -
Viewing PET data in IGV
I have a bed file from PET data in this format
chr17 58754953 58754971 pair1 23 -
chr17 58755650 58755672 pair1 25 +
chr13... -
SAM (from bowtie2) to BAM problem using samtools
I generated a de novo assembly of illumina hiseq reads using Abyss & trans-Abyss, aligned the reads back to the assembly using bowtie2, and am now... -
Problems with display in IGV
Hello everybody,
I hope this is not off topic, I'm new in this forum.
I have installed IGV 2.0.34 on two Windows computers, one 32bit Vista... -
Fusions false positives - using Breakdancer
Dear all,
I'm a phD student with no bioinformatic background.
It's my first post here and hope someone can help me
... -
Fusions false positives - using Breakdancer
Dear all,
I'm a phD student with no bioinformatic background.
It's my first post here and hope someone can help me
... -
IGV: Mapping Quality vs. XA tag (I'm lost)
Hello all,
In IGV, reads with a mapping quality = 0 are displayed in white while reads
with a positive mapping quality are displayed...
