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yjx1217 / simuG

simuG: a general-purpose genome simulator
MIT License
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bwa not generating sam file when provided with simulator's output #1

Closed mrpk123 closed 5 years ago

mrpk123 commented 5 years ago

Hi,

I tried to simulate chr7.fa with 1000 random SNPs with the command

perl simuG.pl -refseq chr7.fa -snp_count 1000 -prefix simulated

Then I tried to generate sam file using bwa. Got following error

image

Would appreciate if you provide any pointers.

Please note, bwa worked very well with the original chr7.fa Regards Mrinal

yjx1217 commented 5 years ago

Hi Mrinal,

Thanks for trying out simuG!
In its current implementation, simuG is for simulating the genome but not the reads, but you can simulate reads using read simulator (e.g. ART for Illumina reads) based on the simulated genome generated by simuG. You can check the supplementary note of our simuG paper for how to do this. After generating the simulated reads, you can map them back to the reference genome to call variants that were introduced by simuG. The supplementary note should also guide you to this point.

Please let me know if you have further questions.

Best, Jia-Xing

mrpk123 commented 5 years ago

Hi Jia-Xing,

Got it. Thank you so much for your prompt reply.

Regards Mrinal

From: Jia-Xing Yue notifications@github.com Sent: Thursday, May 23, 2019 6:06 PM To: yjx1217/simuG simuG@noreply.github.com Cc: Mrinal Puranik mrinal_puranik@persistent.com; Author author@noreply.github.com Subject: Re: [yjx1217/simuG] bwa not generating sam file when provided with simulator's output (#1)

Hi Mrinal,

Thanks for trying out simuG! In its current implementation, simuG is for simulating the genome but not the reads, but you can simulate reads using read simulator (e.g. ART for Illumina reads) based on the simulated genome generated by simuG. You can check the supplementary notehttps://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/PAP/10.1093_bioinformatics_btz424/1/btz424_supplementary_data.pdf?Expires=1558708370&Signature=eDbZ~XgewKxSMTQgIv-KX6~866bMqjmZWzos75HNh~oFBboz8qgKhvWUK11hTy9SxivRoBm3pjJNMFvpGELPpH11mChcjn7w3pkPc3X8~ChcM~1a7tZyXeH1ZImGJV6GVRCQAVId45yJCb7A41mQ3JjC-tZ6fXxdNEq4fiSFZ-lIEdI181r1cD8LMd8cQwVhswCFieDPg9i3Nte015moUXI0D25rsoKRmcQD6hRLJIKWGldWdkHp8b9uDJAKePZpP942qFty3v8fCamcnbN3H05~l1JVrf4UE6uyhcsgwmhIs6LjyCbsr18faXONKNP2p0IIosR4~jLKGtdVeoMpmQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA of our simuG paper for how to do this. Please let me know if you have further questions.

Best, Jia-Xing

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yjx1217 commented 5 years ago

You are welcome! :-) I am closing this issue now.

Best, Jia-Xing