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brentp / goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
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How to generate the X-Y plots? #50

Closed GreeshmaThulasi closed 6 years ago

GreeshmaThulasi commented 6 years ago

Hi all, I have some bam files and corresponding bai files (of unknown gender). I used the indexcov function. But didn't get any X-Y plot. What are the arguments to be supplied for generating X-Y plot. Getting some error as: ngslab@ngslab-OptiPlex-3050:~/Downloads/goleft-master/indexcov/input$ goleft indexcov --directory /home/ngslab/Downloads/goleft-master/indexcov/ '/home/ngslab/Downloads/goleft-master/indexcov/input/NA-180.bam' 2018/10/19 16:18:02 indexcov: running on 1 indexes 2018/10/19 16:18:04 indexcov: found chromosome "chrX", wanted "X" please use exact chromosome names for --sex. 2018/10/19 16:18:04 indexcov: found chromosome "chrY", wanted "Y" please use exact chromosome names for --sex. (WARNING) indexcov: expected 2 sex chromosomes, found: 0. you can set the expected with --sex '' 2018/10/19 16:18:04 sex chromosomes not found. 2018/10/19 16:18:04 got: 1 principal components 2018/10/19 16:18:04 indexcov: 1 principal components, not plotting indexcov finished: see /home/ngslab/Downloads/goleft-master/indexcov//index.html for overview of output Please help me to resolve the issue.

brentp commented 6 years ago

you can use --sex "chrX,chrY" to set the sex chromosomes. if I can make that message clearer, please advise.

GreeshmaThulasi commented 6 years ago

Hi @Brent, Thanks for the help.

Thanks with regards,

Greeshma Thulasi

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you can use --sex "chrX,chrY" to set the sex chromosomes. if I can make that message clearer, please advise.

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