Question: Empty data result from Cufflinks
gravatar for a.walne
8 months ago by
a.walne40 wrote:

Hi I am trying to run Cufflinks on some BAM files that I have generated using HISAT2 with uploaded reference and annotation files. I don't appear to be getting any data in the skipped transcripts tab as shown below. There was also an error message about wrong annotation file type so I followed the suggestion of trying to search again for the file type using the attributes tab

Skipped transcripts 47.14 GB 0 lines formatgtfdatabasehg38 cufflinks v2.2.1 cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 10 -G /jetstream/scratch0/main/jobs/18896476/inputs/dataset_24336832.dat -u -b ref.fa /jetstream/scratch0/main/jobs/18896476/inputs/dataset_24338216.dat

The annotation file URL I uploaded is the genome file URL is:

Is there anything I can do to correct this continuing error, or does it not really matter

Thanks for your help

genome gtf cufflinks custom hisat2 • 222 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by a.walne40
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There are a few items to check:

Tool settings: Did you set the HISAT2 spliced alignment options to report results compatible with Cufflinks?

Data: Your inputs are a match in terms of chromosome identifiers, but this source also includes format, comment, and sometimes fastq lines that will cause problems with the tool.

Alternate method for Data above: Since you are mapping against hg38, and it is a large genome, you might run into memory problems with tools using it as a custom genome. So, instead, you could use the built-in hg38 genome index (if available on the server you are working at) along with a GTF annotation dataset based on the same genome build and that has matching chromosome identifiers.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
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