Display alignment BAM file

Question

[adnan.lahuf]

Dear Colleagues, I am conducting RNA-seq data analysis for an insect. I have used the Bowtie2 tool in Galaxy server to implement the alignment between the RNA-seq data and the complete genome of the studied insect that I downloaded from NCBI. The alignment has done by producing BAM file size 3.4 GB. However, when I tried to display it using IGV or IGB and other tools. I have faced a problem that mainly indicates an important condition which is I should use the Indexed Reference genome of the insect. I have tried to find it for the selected insect but I could not. Thus, could anyone please guide me to resolve this issue?

Best regards Adnan

Answer 1

[GenoMax]

Use the same genome that you used in Galaxy. You can find instructions on setting it up as custom genome in IGV here. (see: creating a .genome file). You minimally need just the fasta format genome file. If you have an annotation file then you can use that as well. Make sure your BAM files are sorted by co-ordinates and are indexed (have .bai file) in order to view them with this custom genome.

Answer 2

[gglim]

Hi adnan,

As GenoMax mentioned, use samtools index to get an index file for your BAM.

For instance

samtools sort insect.bam | samtools index