Tophat fails again and again

Question: Tophat fails again and again

18 months ago by

Hi Jen, I have some problems with one of the dataset and tophat fails again and again. Will you please check it once..??

rna-seq tophat • 392 views

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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by chayanikagoswami.sgt • 0

Would you please send in a bug report from the failed red dataset so I am looking at the correct one? Please make sure both it and the input fastq datasets are undeleted. If there are other jobs (failed or not) with similar content, please also leave those undeleted if possible until I get a copy.

Meanwhile, what happens if you use HISAT instead?

Thanks!

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

Ah, I see the jobs in the existing bug report history (newly added). I'll review, no need to send in another bug report.

We still do recommend moving to HISAT or RNASTAR. Why is explained here: https://biostar.usegalaxy.org/p/23367/

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

18 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

A version of the hg19 genome was selected as the target genome for the failed jobs. These failed jobs also made use of the same hg38-based reference annotation GTF (dataset 9) that was used for the successful jobs mapped against hg38. Try running this failed job against hg38 instead as it appears that is what you intended to do based on the other content of the same history.

If you really did want to map against hg19, then you will need to obtain a reference annotation dataset from UCSC that is based on hg19 and it that for the reference annotation ("known splice sites").

All inputs must be a match for tools to interpret the data correctly. Jobs with mismatched inputs will usually fail but some may produce data that is scientifically invalid. If you ever want to double check what settings were used for a job, the "double-circle" rerun button brings up the tool form view and the "i" info data details button brings up a summary report view.

Hope this helps! Jen, Galaxy team

ADD COMMENT • link modified 18 months ago • written 18 months ago by Jennifer Hillman Jackson ♦ 25k

thank you..now it works..

ADD REPLY • link written 18 months ago by chayanikagoswami.sgt • 0

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