Closed joshuak94 closed 4 years ago
Dear Joshua,
I recommend to use the bwa men command as follows:
bwa mem [indexed reference fasta] [read_1.fastq.gz] [read_2.fastq.gz] -t
Best,
Shunichi Kosugi
2019/09/05 20:09、Joshua Kim notifications@github.comのメール:
Hello,
I'd like to use the scripts here to compare another structural variant caller, Vaquita https://github.com/seqan/vaquita. However, I would like to recreate the datasets as exactly as possible. I've downloaded the same short read sets (data1 to data4), but the paper only says that they were aligned with bwa. Am I right in assuming the following commands:
bwa aln hs37d5.fa ERR174336_1.fastq.gz > ERR174336_1.sai bwa aln hs37d5.fa ERR174336_2.fastq.gz > ERR174336_2.sai bwa sampe ERR174336_1.sai ERR174336_2.sai ERR174336_1.fastq.gz ERR174336_1.fastq.gz > ERR174336.sam — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/2?email_source=notifications&email_token=ADIBV3AIEP6ARQOS7MHZQ2LQIDSG7A5CNFSM4IT4QVYKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HJP757A, or mute the thread https://github.com/notifications/unsubscribe-auth/ADIBV3AIUKBXZP4D5INXLE3QIDSG7ANCNFSM4IT4QVYA.
Thank you! I realized I was using an older version of bwa which didn't have the mem command.
Could you quickly confirm the version used by your group?
The version of bwa we are using is 0.7.13.
Hello,
I'd like to use the scripts here to compare another structural variant caller, Vaquita. However, I would like to recreate the datasets as exactly as possible. I've downloaded the same short read sets (data1 to data4), but the paper only says that they were aligned with bwa. Am I right in assuming the following commands: