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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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Deeptools compGCbias can't handle different chromosome names #65

Closed vivekbhr closed 8 years ago

vivekbhr commented 10 years ago

command for computeGC: /script/computeGCbias --genome mm9

Error: Bam and 2bit do not have matching chromosome names: 2bit:['1', '3', '2', '5', '4', '7', '6', '9', '8', 'Y', 'X', '11', '10', '13', '12', '15', '14', '17', '16', '19', '18', 'MT']

bam:('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chrX', 'chrY')

fidelram commented 10 years ago

Hi,

Does it stop? I think the code should continue, what you see is just a warning.

If you continue to have a problem be sure to have a 2bit file that matches the genome (and chromosome names) that you used for mapping. Making a new 2bit file is very quick.\

Best.

fidel

On Mon, Nov 3, 2014 at 3:26 PM, Vivek Bhardwaj notifications@github.com wrote:

command for computeGC: /script/computeGCbias --genome mm9

Error: Bam and 2bit do not have matching chromosome names: 2bit:['1', '3', '2', '5', '4', '7', '6', '9', '8', 'Y', 'X', '11', '10', '13', '12', '15', '14', '17', '16', '19', '18', 'MT']

bam:('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chrX', 'chrY')

— Reply to this email directly or view it on GitHub https://github.com/fidelram/deepTools/issues/65.

Fidel Ramirez

vivekbhr commented 10 years ago

yah when i use a 2bit file with chr1 .... it works and ignores the discrepancies .. but if i use 2bit without "Chr" i stops

Greetings Vivek

Vivek Bhardwaj Research Scholar Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51, Freiburg

On Mon, Nov 3, 2014 at 3:40 PM, Fidel Ramirez notifications@github.com wrote:

Hi,

Does it stop? I think the code should continue, what you see is just a warning.

If you continue to have a problem be sure to have a 2bit file that matches the genome (and chromosome names) that you used for mapping. Making a new 2bit file is very quick.\

Best.

fidel

On Mon, Nov 3, 2014 at 3:26 PM, Vivek Bhardwaj notifications@github.com wrote:

command for computeGC: /script/computeGCbias --genome mm9

Error: Bam and 2bit do not have matching chromosome names: 2bit:['1', '3', '2', '5', '4', '7', '6', '9', '8', 'Y', 'X', '11', '10', '13', '12', '15', '14', '17', '16', '19', '18', 'MT']

bam:('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chrX', 'chrY')

— Reply to this email directly or view it on GitHub https://github.com/fidelram/deepTools/issues/65.

Fidel Ramirez

— Reply to this email directly or view it on GitHub https://github.com/fidelram/deepTools/issues/65#issuecomment-61486579.

dpryan79 commented 8 years ago

@vivekbhr: Can you check and see if this is still an issue?

dpryan79 commented 8 years ago

I can confirm that this is still an issue.

dpryan79 commented 8 years ago

This means that correctGCbias also can't handle differing names

fidelram commented 8 years ago

Although we can fix the by adding or removing internally a prefix in the chromosome names (as we do in other tools), the workaround is simple. I don't think is a bug.

dpryan79 commented 8 years ago

There will always be edge cases of this, but most of them should be covered by #243