Hi all,
I'm checking reads mapping coverage on rice genome using IGV but find something strange:
(1) I generate .tdf file for IGV using the following command:
igvtools count -z 10 -w 1 a.sorted.bam a.tdf rice.genome
where rice.genome is the genome file generated by igv
(2) I generate coverage file using samtools using the following command:
samtools mpileup -BQ0 -d10000000 -f rice.fasta a.sorted.bam >a.mpileup
However, I find regions where a.tdf shows reads mapped but a.mpileup does not. The following is an example:
a.mpileup (mpileup.jpg) suggests no reads mapped between 16097520 and 16103121
a.tdf (igvtools.jpg) suggests several regions between 16097520 and 16103121 are covered by reads.
Can anybody explain and solve this problem?
Many thanks
Hao
I'm checking reads mapping coverage on rice genome using IGV but find something strange:
(1) I generate .tdf file for IGV using the following command:
igvtools count -z 10 -w 1 a.sorted.bam a.tdf rice.genome
where rice.genome is the genome file generated by igv
(2) I generate coverage file using samtools using the following command:
samtools mpileup -BQ0 -d10000000 -f rice.fasta a.sorted.bam >a.mpileup
However, I find regions where a.tdf shows reads mapped but a.mpileup does not. The following is an example:
a.mpileup (mpileup.jpg) suggests no reads mapped between 16097520 and 16103121
a.tdf (igvtools.jpg) suggests several regions between 16097520 and 16103121 are covered by reads.
Can anybody explain and solve this problem?
Many thanks
Hao
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