Bowtie2 alignment with GRCM39 mouse genome_issue

[zuzerdhoondia]

Hi,

I used two mouse genomes (mm10 and GRCm39) and aligned my fastq files ( Links from Bowtie2 website: https://genome-idx.s3.amazonaws.com/bt/mm10.zip and https://genome-idx.s3.amazonaws.com/bt/GRCm39.zip** ). In comparision, the alignment work same is case with exactly same alignment result. Also, all the downstream processing samtools sort, samtools rmdup, samtools index and bamCoverage went all perfectly fine in both cases. The output from bamCoverage from mm10 was readable in the genome browser IGV and UCSC. However, the output from bamCoverage from GRCm39 was not readable. I did notice that the annotation from alignment and samtools step gave different annotation. Attach images show mm10 labelled as Chr1... ch2...chr3 .....so on but the labels in GRCm39 are with letters NC ...NT....NW and so on. I am confused if the link on the Bowtie2 website indexed for NCBI and UCSC genome differently..? If so is there anyway way I can read files that were aligned to GRCm39 ?

[zuzerdhoondia]

Just wanted to update GRCm38 (https://genome-idx.s3.amazonaws.com/bt/GRCm38.zip) work same as mm10. So the only issue seems with GRCm39. Since, it was the latest genome for mouse...I used it for my sample. However seems there is some issue with index, if I see this problem correctly

.