Question: ChIP-seq mapping with Bowtie for Illumina 1.1.2
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gravatar for saswati.das
3 months ago by
saswati.das0 wrote:

Hi,

I mapped my chip seq data with 'Map with Bowtie for Illumina 1.1.2' and used 'Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region'. The output displays, "An error occurred setting the metadata for this dataset". What does this mean?

Thanks

bowtie bowtie2 chip-seq • 144 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by saswati.das0
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is a much older tool and the metadata may be problematic versus the new bam datatypes. I'll confirm this.

Meanwhile, these are your choices, with the first preferred:

  • Use Bowtie2 instead, the most current version of the tool wrapper. If the older Bowtie is in a workflow, consider replacing it.
  • Click on the link within the dataset to "autodetect" the BAM metadata again - this will usually fix the problem.

Support FAQs: https://galaxyproject.org/support/#troubleshooting

Galaxy Tutorials: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k

Thanks Jennifer. I'll try these options.

ADD REPLYlink written 3 months ago by saswati.das0
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