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Old 11-26-2010, 07:03 AM   #1
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Location: Germany

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Default problems visualizing bam files in IGV


I am aligning RNA-seq data using Bowtie and when I tried to visualize the bam file in IGV, everything is fine except that there are not reads in chrX and chrY. However I have coverage of these chrs because I use the same file for running Cufflinks and I get gene expression in those chrs. I have also checked the hg18.fa.fai which I used for indexing my bam file, and both chrs are included.

Have someone any idea what could be the problem?

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Old 11-27-2010, 03:45 AM   #2
Simon Anders
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Check that the chromosome names are the same in your genome file (as displayed in the drop-down box that allows you to select the chromosome to display in IGV) and in your BAM file (check with 'samtools view'). If it is called, say, 'X' in IGV and 'chrX' in the BAM file, it won't work.

If the names don't match, or if the sex chromosomes are completely missing from the drop-down box, make a new genome file with the "Import Genome" function of IGV, using your genome FASTA file and a corresponding GTF file.
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Old 11-29-2010, 05:33 AM   #3
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I checked it and found that I needed to sort my .bam file and then indexing the sorted.bam file. Now is working!
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Old 04-21-2015, 11:33 PM   #4
Location: Uganda

Join Date: Jan 2015
Posts: 71

Dear all,
I have used bowtie2 to align paired – end illumina reads from cowpea and generated bam files. my next task is to visualise the alignments using igv. how do i proceed without a cowpea enome. My interest is to find out the proportion of reads a matching each of the virus hits.
I am working on a server.
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bam, chrx, igv rna-seq, index

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