Question: coverageBed with -g option ?
0
gravatar for bioguy24
4.0 years ago by
bioguy24190
Chicago
bioguy24190 wrote:

I am running a coverageBed and getting the below error.

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ coverageBed -d -sorted -a /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed -b /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam > /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_output.txt
ERROR: Database file /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam contains chromosome , but the query file does not.
       Please re-reun with the -g option for a genome file.

The newheader.bam is sorted like so:

cmccabe@DTV-A5211QLM:~/Desktop/NGS/pool_I_090215$ samtools view -H IonXpress_008_150902_newheader.bam | grep SQ | cut -f 2 | awk '{ sub(/^SN:/, ""); print;}'
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chrM

 

Since the bam file is uses "human ordering, I sorted the bed file in the same way using the -faidx option in bedtools.

cmccabe@DTV-A5211QLM:~/Desktop/NGS/bed/bedtools$ awk '!_[$1]++' | cut -f1 xgen_targets_sorted.bed | uniq
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY

I am not familiar with the -g option or how to use it.  Is the hg19 file in the /genomes different?  Thank you :).

 

 
bedtools • 1.5k views
ADD COMMENTlink written 4.0 years ago by bioguy24190

I was able to figure it out.... thank you :).

ADD REPLYlink written 4.0 years ago by bioguy24190

Ooh, the suspense is killing me! Was it chrM?

ADD REPLYlink written 4.0 years ago by Joseph Pearson450

Yes it was! :)

ADD REPLYlink written 4.0 years ago by bioguy24190
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