Q about subjunc and fusions

[amisic]

Hello,

I am quite new to RNAseq and I am analyzing a viral dataset (150 bp paired end sequencing on the NextSeq) where I am specifically looking unusual fusion events. I am using subjunc (within the Subreads package) and found several fusion events of interest. However, I am unsure how to open these or process them further. I would like to look at the individual sequences which subjunc used to call the fusions. How would I go about this? The alignment file is supposed to be in a BAM format, but I have been unable to open it. Any suggestions would be much appreciated.

[GenoMax]

Use IGV to inspect your alignment file. BAM files are binary and not directly viewable. You will need to convert them to corresponding text format (SAM) using samtools (check the samtools view command) if you want to view them.

[amisic]

Hi GenoMax,

Thank you for your response. I downloaded IGV. When I try to import the bam files, I'm told I need an index file, but I do not know which file it is or how to make one. I've looked through the manual but I'm unsure how to create an index file for the BAM (or was that an output from Subjunc?) Thank you so much for your assistance.

[GenoMax]

You can index the BAM file with samtools. This will produce a *.bam.bai file. This needs to be in the same directory as your bam when you try to visualize with IGV.

Your BAM file will need to be sorted to allow random access. It is probably not sorted at this time. You should do both these steps before using IGV.

$ samtools sort your_original.bam your_sorted
$ samtools index your_sorted.bam