medhat

Hi, I'm using PBSuite version 15.8.24 Honey.py spots was used to identify structure variations. one line from the output: 1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000 this means that the start of the insertion in the genome is 1211650 and the end 1211854?! is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/),...

Hi, I'm using PBSuite version 15.8.24 Honey.py spots was used to identify structure variations. one line from the output: 1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000 this means that the start of the insertion in the genome is 1211650 and the end 1211854?! is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/),...

Hi, I'm using PBSuite version 15.8.24 Honey.py spots was used to identify structure variations. one line from the output 1 1211650 1211854 INS 353 zscore=-11.943;szMean=353.000;sz3rdQ=550.000;szCount=5.000;strandCnt=2,3;szMedian=547.000;groupName=1;coverage=14.000;sz1stQ=60.000;mqfilt=0.000 this means that the start of the insertion in the genome is 1211650 and the end 1211854?! is not the insertion should happen in one point in the genome (so the start and the end should be the same as in https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/9b263cf1/),...

Hi, I am running Honey.py spots with 10 threads and I have this error: 2017-10-11 14:46:53,098 [INFO] |6:SpotCaller|RateMean 0.060716 -- RateStd 0.238808 [e0129:31253] *** Process received signal *** [e0129:31253] Signal: Segmentation fault (11) [e0129:31253] Signal code: Address not mapped (1) [e0129:31253] Failing at address: 0x1581078 [e0129:31254] *** Process received signal *** [e0129:31254] Signal: Segmentation fault (11) [e0129:31254] Signal code: Address not mapped (1) [e0129:31254] Failing...

created the bam file like this: blasr ./filtered_subreads.fastq ./genome.fa --nproc...

Thanks a lot for answering, According to what you said; First I need to do: java...

fastqToCA -l PacBio -s corrected_pacBio_seq.fasta > new.frg There is no need to -q...

use Celera Assembler with corrected PacBio reads