Question: Problem using bowtie2
gravatar for miguel_000
7 months ago by
miguel_0000 wrote:

Hi everyone I´m Miguel, I´m using galaxy for a scholar research. I´m having a problem using bowtie2 I get this error when I execute.

` The server could not complete the request. Please contact the Galaxy Team if this error persists. Unknown error occurred while processing request.

{ "tool_id": "", "tool_version": "", "inputs": { "library|type": "paired", "library|input_1": { "values": [ { "src": "hdca", "name": "UB40T", "tags": [], "keep": false, "hid": 194, "id": "ae86fb24705b8453" } ], "batch": true }, "library|input_2": { "values": [ { "src": "hdca", "name": "UB4IT", "tags": [], "keep": false, "hid": 195, "id": "b2cb921088839474" } ], "batch": true }, "library|unaligned_file": "false", "library|aligned_file": "false", "library|paired_options|paired_options_selector": "no", "reference_genome|source": "history", "reference_genome|own_file": { "values": [ { "src": "hdca", "name": "genoma", "tags": [], "keep": false, "hid": 204, "id": "0222658b9c7af35d" } ], "batch": true }, "rg|rg_selector": "do_not_set", "analysis_type|analysis_type_selector": "simple", "analysis_type|presets": "no_presets", "save_mapping_stats": "false", "__job_resource|__job_resource__select": "no" } } Close`

image of the error

UB4IT and UB40T are the dataset list of the RNAseq genoma = the dataset list of the chromosomes of the reference genome I´m using (Capsicum annuum/ pepper zunla in this case)

If I execute the bowtie2 using multiple dataset in the reference genome I get this

thanks for your time :)

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by miguel_0000
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The custom genome needs to be reformatted:

1 - Mismatch between the reference genome and the reference annotation

The identifier/annotation on the title line for the fasta sequences are currently like this:

>gi|404474503|ref|NC_018552.1| Capsicum annuum chloroplast, complete genome

But the reference GFF has the "chromosome" names like this:


These need to be an exact match. Meaning, for this reference genome sequence, the fasta must have a title line like:


2. The custom reference genome is split into several datasets.

These should be merged into a single dataset. Use the tool Concatenate to stack the individual datasets together. Then check for empty lines and reformat the sequence wrapping just to be sure all is consistent.

Custom genome FAQs

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
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