htseq-count with gff error

Question: htseq-count with gff error

3.8 years ago by

jchen015 • 80

Singapore

jchen015 • 80 wrote:

Dear all.

Please take a look at my errors: http://goo.gl/Oa2IxR

In the link, you will see 2 images (1.png and 2.png).

1.png shows that i am trying to make use of HTSeq-Count to get the read-count for a specific gene.

2.png shows the error when Executed.

I downloaded the gff file online from ensembl link (http://www.ensembl.org/info/data/ftp/index.html) and my .bam file contains hg19 data. Please advise why this error occurs...

Do I have to add to my python path or something? or my root path.

Thank you guys for the time, appreciate it.

Regards,

Julius

gff htseq-count • 2.3k views

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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by jchen015 • 80

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There is a reference genome mismatch issue between the inputs. Specifically, the chromosome identifier are different. Consider a reference annotation dataset from UCSC or iGenomes, or you can see if the conversion help in the wiki works for you case.

http://wiki.galaxyproject.org/Support#Reference_genomes
http://wiki.galaxyproject.org/Support/ChromIdentifiers

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Dear Jennifer

Thanks for the reply. Now I know what is the issue...

May I check with you, if i were to download a reference annotation dataset from UCSC, it will probably be accessible via this link (http://hgdownload.cse.ucsc.edu/downloads.html#human). But however, i would require a gtf/gff annotation dataset because HTSeq-Count requires it.

Will there be an available download link for me to download such a annotation dataset (for hg19) anywhere in the portals?

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

Try using the tool "Get Data -> UCSC Main" to access the same information. GTF output is an option for most primary tracks. This will load the data directly into your history, if you leave the "Galaxy" button checked on the UCSC Table browser form for where to send the output (is checked by default through this tool). Best, Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer

Thanks for the recommendation. I proceeded with your advice and managed to get the annotation file sent to my local galaxy server.

However, the error still persist. What could possibly be the reason?

Error: http://goo.gl/UhaNxq (As shown on instruction 21, the annotation file has successfully uploaded)

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

Hello - did you install this from the Main tool shed (http://usegalaxy.org/toolshed) using managed dependencies (this is the default setting)? If not, or just to double check, make sure that the binary and the wrapper are based on the same tool version. This looks like a mismatch to me. If after checking there is still a problem, send in the error to the tool developers (through the tool shed). This is an IUC tool, so they will want to know if there is a problem. Thanks, Jen

ADD REPLY • link modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer

Install this? What do you mean? Anyway, the link is broken...

ADD REPLY • link written 3.8 years ago by jchen015 • 80

Thanks! I fixed the link. By install, I mean when you installed the htseq count wrapper into your local Galaxy. Did you use the managed dependencies options? Have you compared the binary version on your machine to what the wrapper is expecting to use? Jen, Galaaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hey Jen.

Thanks for the reply!

Yes I would believe I did used teh managed dependencies option (as shown here: http://goo.gl/drO6P2).

How can i compare the binary version of my machine to the wrapper it is expecting to use?

I am really sorry for this as I have no idea how to manipulate with the Galaxy tools and functions..

Regards,

Julius

ADD REPLY • link written 3.8 years ago by jchen015 • 80

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