Extract spanning reads and junction reads around integration site about vicaller HOT 3 CLOSED

Hi Yang,

Thanks for your interest.

1. You can find out the read ID from the file seq.virus_f2 (column 31, e.g. read_200_3266186|1|read_200_1803970|1|read_200_6441240|1), the supporting reads of all VIs in FASTQ format can be found in seq_1.1fuq, seq_2.1fuq, and seq_sf.1fuq (split reads).

2. seq.CS3 can also be produced after the running of the validation function per VI. After you run it, the supporting reads will be separate by each validated VI location.

Best,
Xun

from vicaller.

Thx for your response.

There are some difference between reads reported in .1fuq and .output. The manual suggested the reads reported in .1fuq are potential. Could you please give me some details about the potential? The soft-clip part of reads are larger than 20 bp?

Another question is for the .visulization file. The seqs reported are not the same in the specific region. For example, the region of human part started from 43200, all the seqs reported are very different to each other. To my understandings, the visulization file suggested these seqs shared this region.

Cheers,

Yang

from vicaller.

Sorry for my late reply.

As you said, reads reported in .1fuq are potential. So you can use the read ID reported in the seq.virus_f2 file as i mentioned previously to extract the read sequences.

The soft-clip part of reads are larer than 20 bp.

For the .visualization file, you can use the start and end position and reported GI in the .output file to extract corresponding records in the .visualization file. PS: make sure the reference build is the same. The current example output is using hg19 as reference.

You also can send me the .output file and .visualization file to my email, I will be more than happy to check it out.

Cheers,
Xun

from vicaller.