Question: Tophat fails again and again
0
gravatar for chayanikagoswami.sgt
10 months ago by
chayanikagoswami.sgt0 wrote:

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 • 195 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson24k • written 10 months ago by chayanikagoswami.sgt0

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 REPLYlink written 10 months ago by Jennifer Hillman Jackson24k

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 REPLYlink written 10 months ago by Jennifer Hillman Jackson24k
0
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson24k

thank you..now it works..

ADD REPLYlink written 10 months ago by chayanikagoswami.sgt0
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