Closed linatbeishan closed 8 years ago
Hi, For the first part, perhaps you could provide me more information about your settings, such as the version of bwa, the quality score threshold, ...
About the last 2 parameters in 'config.txt', you may just use the default "151 and 500", unless the length of your sequencing data is longer than 151, or the fragment size is longer than 500. These 2 parameters decide the size of the pseudo-references, please make sure that they are big enough for your data.
The next update would only upgrade the user interface, the detection algorithm would not be changed.
Thanks! :-)
Thanks, tw.
Here are the softwares, data and script I used, hope this helps. 1. Softwares: bwa: 0.7.12-r1039; samtools: 0.1.19-44428cd bedtools: bedtools-2.24.0 blat: (version:NA, last modified: 2016-02-16) http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/ novoalign: V3.04.01 2. Both reference and index are downloaded from the ftp: ftp://treeslab1.genomics.sinica.edu.tw/NCLscan/ 3. The script used: ./NCLscan.sh simu_5X_100PE_1.fastq simu_5X_100PE_2.fastq test_NCLscan 0 3 50 2>&1 | tee test_NCLscan.log
linwei
Please try the latest version(v1.6) of NCLscan.
Hi, I have 2 questions regarding to this software(v1.4).
Thanks!