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


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?


bowtie bowtie2 chip-seq • 62 views
ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson25k • written 4 weeks ago by saswati.das0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

Galaxy Tutorials:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson25k

Thanks Jennifer. I'll try these options.

ADD REPLYlink written 4 weeks ago by saswati.das0
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