Using filtered data for TopHat

Question: Using filtered data for TopHat

2.0 years ago by

kuk2 • 20

kuk2 • 20 wrote:

Hi,

When I extract DRR data using "Extract reads in FASTQ/A format from NCBI SRA," for TopHat, I was able to get both a bam file and bam-index file.

However, when I filtered the extracted reads in FASTAQ format using "Filter FASTQ reads by quality score and length" and used the filtered data for TopHat, I was not be able to get the bam-index file and got the following error message, "An error occurred setting the metadata for this dataset Set it manually or retry auto-detection."

I repeated this twice, and I got the same message. Please let me know if you have any suggestion to fix this error.

Thanks,

kazz

error tool main usegalaxy.org tophat • 745 views

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modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.0 years ago by kuk2 • 20

Is your FASTQ file after the filter step still valid? For example if your file would be empty you can get such an error, because no index could be created.

ADD REPLY • link written 2.0 years ago by Bjoern Gruening ♦ 5.1k

Is your FASTQ file after the filter step still valid? For example if your file would be empty you can get such an error, because no index could be created.

ADD REPLY • link written 2.0 years ago by Bjoern Gruening ♦ 5.1k

2.0 years ago by

kuk2 • 20

kuk2 • 20 wrote:

Hi,

The file is not empty. When I tried to make the bai file from the link "Set manually and auto-detection" and then "Convert Format," I was able to make a bai file, and I was able to see the bam file using igv.

However, when I was analyzing a different data set (this time I used the original DRR data, not filtered) again, I got the same error (no bai file made) again (I tried twice, and I got the same error message; this situation is exactly the same as my first question). So I tried to make the bai file using the same command (Convert Format). Although this new data set was added to queue four days ago, it has never been processed, and I only get the following message, "This is a new dataset and not all of its data are available yet."

This new data set does not appear to be empty, either, since I can see some sequences and scores in the file.

I have no idea why this data set does not begin to be processed for such a long time. Please give me your suggestion to fix this problem. Thanks,

kazz

ADD COMMENT • link written 2.0 years ago by kuk2 • 20

2.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are some issues with Galaxy Main at http://usegalaxy.org. This may have impacted jobs as of late Weds and now is manifesting as temporary downtime (two distinct issues). Please follow here for details and updates: https://biostar.usegalaxy.org/p/20698/

Our apologies for the inconvenience, Jen, Galaxy team

ADD COMMENT • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k

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