Hello,
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?
Thanks
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?
Thanks
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