Bed file loading issues
1
1
Entering edit mode
8.7 years ago
skbrimer ▴ 740

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?

igv Bed • 6.2k views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
8.7 years ago
skbrimer ▴ 740

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2253 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6