using SAF gene annotation file in featurecounts

Question: using SAF gene annotation file in featurecounts

18 days ago by

ivycm • 20

ivycm • 20 wrote:

Hello!

I'm new to Galaxy and was wondering if I could get some help with using the featurecounts tool! All of my mapped data is currently in BAM format and now I am looking to use featurecounts to measure gene expression. The species I'm working on doesn't have the gene annotation file built into Galaxy, so I was given an annotation file from some collaborators to use, which is in SAF format. I understand that if I upload an annotation file to my project that it will only be recognized if it is in gff format, despite the built in annotation files being in SAF format. Is there any way that I can run this SAF gene annotation file (as SAF format) in featurecounts? If not, how should I go about dealing with this?

Thank you!

featurecounts saf galaxy • 58 views

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modified 15 days ago by Jennifer Hillman Jackson ♦ 25k • written 18 days ago by ivycm • 20

15 days ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

SAF format is not supported at this time when it is selected from the history. You'll need to convert the SAF data to GTF. It takes a few steps to get this right, so I created and published a workflow at Galaxy Main (anyone can use it). I tried to make it as general as possible. You can import your own copy, give it a test run, then edit it as needed to suit your data.

https://usegalaxy.org/u/jen/w/saf-to-gtf

The SAF test data I ran through it was sourced from the Featurecounts help here: https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts

Note: I made a few assumptions about formatting. This GTF will (or should) work with Featurecounts but may not work well with other tools as there are no transcript features or identifiers. The only attribute data (9th column) is "gene_id". If you can find a GTF file for your genome on your own, that would be a better choice, but sometimes those are not available.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 15 days ago by Jennifer Hillman Jackson ♦ 25k

Yay! Thank you so much! This worked!

ADD REPLY • link written 15 days ago by ivycm • 20

Great, glad this had a successful result!

ADD REPLY • link written 14 days ago by Jennifer Hillman Jackson ♦ 25k

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