bedtools genome file

Question

[tom]

Hello,

I have some issues with bedtools genomecov. My goal is to produce bedgraph outputs from bed files using bedtools genomecov. With bed files as input, it requires a genome file. I got it from uscs table browser. It is a tab-delimitated file with 3 columns : chr / size / filename I removed the third one and the first line that contains the names of the column but I get an error message from bedtools :

". Exiting...illegal number" 32079331

32079331 is the size of the first chromosome When I add an empty column using tabulation after 32079331, then it recognises the first chromosome but not the following one. So I added an empty column after each chromosome. When It comes to the last one however, I get another error message :

Unexpected file format. Please use tab-delimited BED, GFF, or VSF. Perhaps you have non-intger starts or ends.

I changed the format from .genome to .bed but it does not change anything.. I don't understand. I hope someone can help. Thank you very much in advance!

[Pierre Lindenbaum]

what is the output of

$ head your.bed
$ file your.bed

[tom]

head your.bed

3R      11350651        11350750        3R      11350684        11350783        K00201:460:HK7VGBBXY:7:2101:1580:48931  44
3R      27784656        27784723        3R      27784657        27784724        K00201:460:HK7VGBBXY:7:2101:1580:49036  44
X       21281305        21281349        X       21281306        21281350        K00201:460:HK7VGBBXY:7:2101:1590:33369  44
X       2080929 2080979 X       2080930 2080980 K00201:460:HK7VGBBXY:7:2101:1590:34565  44      +       -
3L      4194605 4194704 3L      4194637 4194736 K00201:460:HK7VGBBXY:7:2101:1590:34670  44      +       -
3L      3238904 3239001 3L      3239001 3239100 K00201:460:HK7VGBBXY:7:2101:1590:35444  44      +       -
.       -1      -1      .       -1      -1      K00201:460:HK7VGBBXY:7:2101:1590:35972  0       .       .
X       7642046 7642137 X       7642047 7642138 K00201:460:HK7VGBBXY:7:2101:1590:39137  44      +       -
3L      25131745        25131844        3L      25131839        25131937        K00201:460:HK7VGBBXY:7:2101:1590:39699  11
2R      12090329        12090428        2R      12090402        12090499        K00201:460:HK7VGBBXY:7:2101:1590:40965  44

file your.bed

18dm6.bed: ASCII text

Here are the outputs. There was a mistake in chromosome name... In one file, called chr3R in the other 3R. Now it seems to work except that the tool encounters problem line 7. No idea what that line means and where it comes from.

I am wondering why I had to add a tabulation after each line of the genome file to make it work?

[Pierre Lindenbaum]

not a bed line:

.       -1      -1      .       -1      -1      K00201:460:HK7VGBBXY:7:2101:1590:35972  0       .       .

[tom]

Yes, I do not know where it comes from.. I will start from new. Maybe I did a mistake at some point.

Thank you!

[Pierre Lindenbaum]

unmapped read ?

[tom]

Yes, that's what I thought too, so i am now running bowtie2 again with --no-unal option.