Help with making tdf file with bed file as input

[Sheila Teves]

Hello,

I was trying to make a tdf file with a bed file as input. I got an error of "No features were found that matched chromosomes in genome: /Users/sheilateves/Desktop/IGVTools/genomes/hg19" When I did this command from the original bam file, it worked. The original bam file contained all reads, then I parsed the reads based on fragment size, and converted the parsed reads into bed files. Now I want to make a tdf file to visualize the size-parsed reads.

Here's my command:

~/Desktop/IGVTools/igvtools count -w 50 --pairs Ad2_3_S3_hg19.20_100_sorted.bed Ad2_3_S3_hg19.20_100_sorted.tdf hg19

I got this error:

INFO [2017-06-15 11:35:49,479]  [IgvTools.java:777] [main]  Computing coverage.  File = Ad2_3_S3_hg19.20_100_sorted.bed

Computing coverage.  File = Ad2_3_S3_hg19.20_100_sorted.bed

INFO [2017-06-15 11:35:49,482]  [IgvTools.java:778] [main]  Max zoom = 7

Max zoom = 7

INFO [2017-06-15 11:35:49,482]  [IgvTools.java:779] [main]  Window size = 50

Window size = 50

INFO [2017-06-15 11:35:49,483]  [IgvTools.java:784] [main]  Window functions: mean 

Window functions: mean 

INFO [2017-06-15 11:35:49,483]  [IgvTools.java:785] [main]  Ext factor = 0

Ext factor = 0

INFO [2017-06-15 11:35:49,490]  [GenomeManager.java:130] [main]  Loading genome: /Users/sheilateves/Desktop/IGVTools/genomes/hg19.chrom.sizes

Loading genome: /Users/sheilateves/Desktop/IGVTools/genomes/hg19.chrom.sizes

INFO [2017-06-15 11:35:49,549]  [DirectoryManager.java:149] [main]  IGV Directory: /Users/sheilateves/igv

IGV Directory: /Users/sheilateves/igv

INFO [2017-06-15 11:35:49,566]  [GenomeManager.java:174] [main]  Genome loaded.  id= /Users/sheilateves/Desktop/IGVTools/genomes/hg19

Genome loaded.  id= /Users/sheilateves/Desktop/IGVTools/genomes/hg19

WARN [2017-06-15 11:36:07,307]  [Preprocessor.java:314] [main]  No features were found that matched chromosomes in genome: /Users/sheilateves/Desktop/IGVTools/genomes/hg19

No features were found that matched chromosomes in genome: /Users/sheilateves/Desktop/IGVTools/genomes/hg19

100.0% 

Done

The bed file is sorted and looks like this:

chr1 10000 10048 48

chr1 10002 10054 52

chr1 10002 10065 63

chr1 10002 10071 69

chr1 10003 10066 63

chr1 10003 10066 63

chr1 10003 10066 63

chr1 10003 10066 63

chr1 10003 10072 69

chr1 10003 10084 81

Any ideas?

Thanks!

Sheila

[James Robinson]

Could you attach a portion of your bed file?  Maybe the first 100 lines.   Pasting into email or a forum post doesn't work because whitespace isn't preserved properly.

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[Sheila Teves]

I've attached the first 100 lines of the bed file. Thanks!

Sheila

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[James Robinson]

Hi,  I am not sure why, but the --pairs argument is causing the problem.  --pairs only applies to Bam files,  so it is not needed,  leave it off and it should work (it does for me).    I will investigate further the misleading error message.

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[Sheila Teves]

Ok, thanks. I'll try it without the --pairs option