Thanks,
If I use bowtie, does it make any difference in alignment.
When I am running cmd with bowtie, while processing it shows below message:
CMD: bowtie -k 20 -S --sam-nohead -q target single_fa > single_fa.pre.sam
Upto my understanding it says sam has no header. Am I correct?
when i run stat.pl cmd to obtain read alignment statistics:
result shows:
read_type count pct
single 6874526 100.00
but no information about proper and improper pairing.
Hope you can shed lights on this.
Thanks a bunch.
Naresh
If I use bowtie, does it make any difference in alignment.
When I am running cmd with bowtie, while processing it shows below message:
CMD: bowtie -k 20 -S --sam-nohead -q target single_fa > single_fa.pre.sam
Upto my understanding it says sam has no header. Am I correct?
when i run stat.pl cmd to obtain read alignment statistics:
result shows:
read_type count pct
single 6874526 100.00
but no information about proper and improper pairing.
Hope you can shed lights on this.
Thanks a bunch.
Naresh
Originally posted by westerman
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