Can IGV be used to visualize Mitogenome readpools

Question

[F.I.2011]

Hello everyone,

I am struggling to use IGV to visualize my readspools against my reference Mitogenome. It is avian mitogenome. I upload new genome by downloading FASTA and GFF3 file.

For the workflow:

I convert paired end reads (R1 and R2) into bam file by this command:

java -jar ----picard.jar' FastqToSam F1=FQ-R1.fastq F2=FQ-R2.fastq O=.bam SM=GK-2 RG=null

sorted by :

SortSam \I=GK-2.bam \ O=GK-sorted.sam  \ SORT_ORDER=coordinate

and build Index by BuildBamIndex.

But when I uploaded that bam file against my own-made genome file, i had no reads and zero coverage. Here is the image of IGV after uploading bam files

Then I sorted bam with queryname SORT ORDER by this command

SortSam \I=GK-2.bam \ O=GK-sorted.bam  \ SORT_ORDER=queryname.

but then BuildBamIndex gave error and need to sort bam file with coordinate SORT ORDER not queryname and IGV also denied to upload file without index file.

Please need help me to fix it. Can I use IGV for small 17000 genome that dont have inbuilt reference genome.

Thanks

Answer 1

[Benn]

The FastqToSam tool makes an unaligned BAM file. For IGV you need aligned reads, so align (with e.g., bwa) your paired-end reads to your genome first, and use that bam file in IGV.