CyVerse HISAT2 output

Question

[phamh]

When I ran HISAT2 on CyVerse, my input files were the reads (read 1 and 2) that needed aligning and the reference genome. The file type was paired end. After the analysis completed, my output files' names appeared to associate with read 1 only.

For example:

• input read 1 = L006_R1_001.fastq.gz
• input read 2 = L006_R2_001.fastq.gz
• output = L006_R1_001.sorted.bam & L006_R1_001.sorted.bam.bai

Can anyone please explain this? Can I assume that even though the names of the files are associated with read 1 only, within the files, there's information on both read 1 and 2?

[GenoMax]

You may want to direct these questions to cyverse support to get proper support.

Assuming that you actually did get a BAM file, it is possible that cyverse may have used the file name for R1 (part before .fastq.gz) to come up with the name for your final BAM file.

[phamh]

I did, but their response was not very helpful, which is why I've posted my question here.

[GenoMax]

Since you are using a GUI based online tool your best bet is to get support from tool owners. Only they know how the tool is implemented on their server. We are going to be guessing most of the time, like I did in my comment above.

[phamh]

Okay. Thank you for your help!