Bed file loading issues

Question

[skbrimer]

Alright, that didn't take long. So I made my script to make my bed file which worked.

Track name=G_anatisUMN179 description=G_anatisUMN179 genes
G_anatisUMN179_dna    0    2687335    UMN179_RS12665    +
G_anatisUMN179_dna    210    1068    UMN179_RS00010    +
G_anatisUMN179_dna    1167    1980    UMN179_RS00015    -
G_anatisUMN179_dna    1972    2215    UMN179_RS00020    -
G_anatisUMN179_dna    2285    2618    UMN179_RS00025    +
G_anatisUMN179_dna    2671    4069    UMN179_RS00030    +
G_anatisUMN179_dna    4188    5592    UMN179_RS00035    -
G_anatisUMN179_dna    5861    7073    UMN179_RS00040    +
G_anatisUMN179_dna    7241    8294    UMN179_RS00045    -
G_anatisUMN179_dna    8309    9716    UMN179_RS00050    -
G_anatisUMN179_dna    9768    10383    UMN179_RS00055    +
G_anatisUMN179_dna    10460    10676    UMN179_RS00060    -
G_anatisUMN179_dna    10647    11184    UMN179_RS00065    -
G_anatisUMN179_dna    11294    11600    UMN179_RS00070    -

4 mandatory columns ripped right from the genbank file, however when I try to load the file into IGV I get the following error.

Error loading /home/sbrimer/genomes/G_anatisUMN179.bed: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@42f867b5, for input source: /home/sbrimer/genomes/G_anatisUMN179.bed

I've tried googling the error and looking into the igv-help group on google but I'm not really finding an answer, did I format my file incorrectly or what step did I miss?

[Devon Ryan]

Try fixing the Track line to:

Track name="G_anatisUMN179" description="G_anatisUMN179 genes"

If that doesn't solve the problem then just subset the file until you can narrow down which line is causing this. That should indicate where the problem is.

[skbrimer]

Thank you for the suggestion, I fixed the script so it makes the header name and description have quotation marks and that did fix the problem. So I started with the subsets, first I did just the header and got the same error. Then I thought it might need more than just the header so I added the first bed line which is the entire genome length and got the same error.

So apparently IGV does not like the file format at all. I will re-read the bed file documentation and keep working on it but thank you for your help.

Answer 1

[skbrimer]

So besides having the header off, it turns out that the bed file I generated from the genbank file had a different id then the fasta version I download as originally to do the alignements. So, in the future I have learned to use the script from the start and I have have become very, very familiar with the BED formate.