Re: [igv-help] Issue with IGV reads display

[Jim Robinson]

The read length it the length of the read, the # of bases in the read sequence.   If you look at the cigar string 142 bases have been soft clipped, and 9 bases aligned,  so 151 total. 

On 7/21/16 4:35 PM, Evergreen wrote:

Hello all,

I just recently came across with IGV for some bam files and found the incorrect display for the read length. I've attached the view blow. Obviously the read length is short, only 9bp. However, while I mouse-over the read, it shows 151bp. 

The bam file has been filtered by the read length which allo should greater than 45bp. I have confirmed to extract the read lengths of all reads and they are all above the threshold. With the converted the fasta file (from bam) and I couldn't find either the read name or the 9bp sequence. 

Has anyone have same issues? Any advice?

Thank you!

Kath

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