i have been trying to convert gtf file to bed12 file but was getting error for the same.
We’ll need more details to help.
From what you explain, this is what to reply with:
- What tool are you using? gffread will produce a BED6, not BED12
- Is the GTF formatted Ok? headers # would cause problems, so remove those first
- If you are incorporating other files, do all the identifiers in common match up?
- What are the error messages? stdout, stderr, sometimes the job info
- What server are you working at? Can you share a history link back?
i Have submitted a gtf file for Plasmodium vivax Sal I for which i need the bed file format. i want the following bed file headers for the gtf file(attached herewith):
| Terms | Description |
|---|---|
| chrom | The name of the chromosome on which the genome feature exists. |
| For example, “chr1”, “contig1112.23”. This column is required. | |
| start | The zero-based starting position of the feature in the chromosome. |
| The first base in a chromosome is numbered 0. This column is required. | |
| end | The one-based ending position of the feature in the chromosome |
| name | Defines the name of the BED feature |
| score | The UCSC definition requires that a BED score range from 0 to 1000, inclusive. |
| strand | Defines the strand - either ‘+’ or ‘-‘ |
| thickStart | The starting position at which the feature is drawn thickly. |
| thickEnd | The ending position at which the feature is drawn thickly. |
| itemRgb | An RGB value of the form R,G,B (e.g. 255,0,0) |
| blockCount | The number of blocks (exons) in the BED line |
| blockSizes | A comma-separated list of the block sizes. |
| blockStarts | A comma-separated list of block starts. |
| The gtf file was download from below url |
Thanks for sharing the BED12 specification you want for the output, that looks standard.
Next, you’ll need to provide more details about your GTF content (screenshot of the top 10 lines or so?) and the tool you are using, the settings applied, and the error.
1.I HAVE ATTACHED THE SCREENSHOT OF THE GTF FILE.
2.I AM USING THE GALAXY TOOL i.e. GTF to BED12(Galaxy Version 357).
3.I am attaching the error code here.
Great, thank you for posting the extra details.
Your GTF data does have header lines. Try removing those, then rerun.
What to do → Remove the headers with the Select tool using the option “NOT Matching” with the regular expression: ^#
If that is not enough, please post back the parameters used for the job. Find those on the Dataset Details view, right above where the logs are located. Expand the datasets to show the metadata and peek view.
The first FAQ I sent explains exactly where to find that: by clicking the 
icon within dataset. That provides more details than the bug icon, and is always a good place to review, for any failure.
1.I HAVE REMOVED THE HEADERS OF THE GTF FILE(ATTACHED HEREWITH) AND HAVE RUN THE TOOL.
2. I HAVE SUCCESSFULLY RUN THE TOOL WITH THE FOLLOWING CHNAGES IN THE PARAMETER.CAN YOU PLEASE GO THROUGH THE PARAMETERS ONCE AND LET ME KNOW WHETHER THEY ARE CORRECT OR NOT (ATTACHED HEREWITH).
3. IN THE BED FILE THAT I GOT, IN THE NAME SECTION THERE IS WRITTEN AS UNASSIGNED TRANSCRIPT(ATTACHED HEREWITH).
4.HOW TO CROSS CHECK WHETHER THE BED FILE I GOT HAS ALSO THE INFORMATION OR NOT.
It sounds like you have a result now, not an error.
You could try different settings to see what those produce. Start with the defaults, then layer changes on and compare.
Glad you got this working!