Good morning,
I am trying to map simulated reads generated from GemSIM to an index generated from a multi-fasta of the CLJU (bacteria) coding sequence from NCBI. I used these two commands and discovered there were no alignment lines in the SAM file, only header lines. Commands head and tail only returned lines starting with @, and grep -vnm1 '^@' returned nothing.
bwa-0.7.3a/bwa index -a is -p CLJU ./CLJUcoding.fasta
bwa-0.7.3a/bwa mem CLJU CLJUsimreadsCodeTrial.single.fastq > CLJUsimreadsCodeTrial.single.sam
Any suggestions?
Thanks and God bless,
Jason
I am trying to map simulated reads generated from GemSIM to an index generated from a multi-fasta of the CLJU (bacteria) coding sequence from NCBI. I used these two commands and discovered there were no alignment lines in the SAM file, only header lines. Commands head and tail only returned lines starting with @, and grep -vnm1 '^@' returned nothing.
bwa-0.7.3a/bwa index -a is -p CLJU ./CLJUcoding.fasta
bwa-0.7.3a/bwa mem CLJU CLJUsimreadsCodeTrial.single.fastq > CLJUsimreadsCodeTrial.single.sam
Any suggestions?
Thanks and God bless,
Jason
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