SInC simulator Activity
An accurate & fast error-model based simulator for SNPs, Indel & CNVs
Status: Beta
Brought to you by:
binaypanda
Activity for SInC simulator
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Katerina Pal posted a comment on discussion General Discussion
Hello! I want to simulate CNVs in targeted exome genes. How can I do that? I’m confused with the readme file. Thanks in advance!
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Stephan Schmeing posted a comment on discussion General Discussion
I did not find a way to include base calling errors into the simulation. I can only provide variants. Did I miss something or is it not supported?
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Thomas Davis posted a comment on discussion General Discussion
Not sure if this forum is still active, but I've noticed what I think may be a bug in SINC's CNV generation, which can cause the CNV start and end listed in the CNV results benchmark file output by SINC, to be off by several thousand bases for chromosome sized inputs compared to the true CNV start and end. I used SINC with CNV parameter (-p) of 8 percent on hg19 chr20, (sequence from here: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/), generated reads with SINC readgen, and aligned...
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Patrick Monnahan modified a comment on discussion General Discussion
I originally posted this comment because I was getting confusing results from SInC_readGen. However, I have realized that it was an issue with running multiple SInC_readGen jobs at once. It seems that the different jobs were writing to the same temporary files, which resulted in output files containing varying numbers of reads and non-matching read pairs.
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I posted a comment earlier, but realized there was an error that I had overlooked. The full error log is below: ======= Backtrace: ========= /lib64/libc.so.6(fortify_fail+0x37)[0x35e29027f7] /lib64/libc.so.6[0x35e29006e0] /lib64/libc.so.6[0x35e28ffb39] /lib64/libc.so.6(_IO_default_xsputn+0xc9)[0x35e28744a9] /lib64/libc.so.6(_IO_vfprintf+0x41c0)[0x35e2848000] /lib64/libc.so.6(vsprintf_chk+0x9d)[0x35e28ffbdd] /lib64/libc.so.6(sprintf_chk+0x7f)[0x35e28ffb1f] ./SInC_readGen[0x4013ca] /lib64/libc.so.6(libc_start_main+0xfd)[0x35e281ed1d]...
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I recently ran SInC_readGen, resulting in two fastq files, which I assume are the files corresponding to each read pair. However, when I attempt to map the reads (using bwa), I get two errors that the files are of different sizes and the paired reads have different names. I confirmed that this was true upon further inspection of the bams. The files differ by 100 million lines, and I can't find corresponding read pairs across the files. I received some errors during the runs, but I don't think these...
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DHLI modified a comment on discussion General Discussion
Hello, After running the sinc, i got the simulated variant result (gold standard...
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Hello, After running the sinc, i got the simulated variant result (gold standard...
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Abdelrahman Hosny posted a comment on discussion General Discussion
I went through the three steps to generate CNVs. However, it looks like the resulting...
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Saurabh Gupta posted a comment on discussion General Discussion
No problem. (y)
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It's working now ! Thank you very much ~! 2016-04-19 18:54 GMT+09:00 Saurabh Gupta...
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0 and 1 differentiates R1 and R2. But I guess bwa requires /0 and /1 instead of _0...
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sorry, i mean change the last character in each line that starts with @ in fq file...
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Hi, Looks like somehow I missed your previous message. You are right, 2 files correspond...
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Hi , i think some part of question have been solved, but some not, After i generated...
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Thank you for your suggestion, the SInC_readGen error also have been solved ! I check...
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Good to hear you could solve SInC_simulate error. For genProfile, you need to give...
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Thank you for your reply ~! Yes , GSL have installed and for the first error have...
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Do you have GNU Scientific Library (GSL) installed?
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Hi Donghe, Thank you for your interest in SInC. We will look into this and get back...
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Hi, I am trying to use SInC simulator to generate indel reads, but i get some error...
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Hi, sorry for the late reply. Input to SInC_readGen is a "fasta" file, it seems you...
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medhat posted a comment on discussion General Discussion
I have these results after using this command ; ./SInC_readGen -C 5 -T 10 -R 100...
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using this command ./genProfile -R 1 -l 100 input.txt where is the input.txt contains...
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using this command ./genProfile -R 1 -l 100 input.txt where is the input.txt contains...
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using this command ./genProfile -R 1 -l 100 input.txt where is the input.txt contains...
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SInC simulator released /SInC_readme.txt
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Hi KosAL, I believe the ref.fasta path that you are giving is very big, currently...
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Hi KosAL, Can you tell me what ref.fasta are you using? And please share the details...
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KosAL posted a comment on discussion General Discussion
Hi, I want to try the SInC simulator but it is aborting at the SInC step. In detail,...
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