how to sort out mate no mapped reads

[hujiacun]

Hi,
I am now doing some analysis about chromosome structure Viaration. Please help me about following questions.
1. Is there any method to sort out reads which mate is no mapped by IGV dispaly. I have dreamed that pair end all mapped reads are not displayed, so I could see what I wanted.
2.If IGV can't do it, is there any methods to sort out single mapped reads from SAM or BAM files. As to the sinle mapped reads,some single mapped reads may scatter around the genome, some may concentrated on one loci. the later situation may reflect a real SV. So is there any method to find concentrated single mapped reads.

[diego diaz]

with samtools you can perform the analysis :

if you have paired-end reads : "samtools view -f 8 -F 4 file.bam" will give you mapped reads with unmapped mate.

if you have unpaired + paired reads: "samtools view -F1 file.bam" will give you unpaired mapped reads

reads concentration, as you say, means deep coverage. To check the coverage along the genome you could use genomeCoverageBed:

genomeCoverageBed -ibam sortedBamFile.bam -g genome.txt > coverage.txt

Paired reads with a bad insert size or mis-oriented also could be evidence of structural variation.

please see this image:

http://genomebiology.com/2008/9/3/R55/figure/F2?highres=y

When you map your reads to some reference you will see similar patterns in regions with structural variation.

[hujiacun]

fastq indicate "table not found"

Who can tell me why err like this after I enter "fastq-dump -X 5 -Z SRR616966"
2015-04-13T15:23:47 fastq-dump.2.1.7 err: table not found while opening manager within database module - failed to open 'SRR616966'