Hello everybody,
I'm quite newbie with bioinformatic, so please forgive me if this is a silly question.
Currently I'm align my reads (100bp, single end) against a .fasta containing a list of viruses (ref seq from NCBI). I'm using bwa (sampe)
If I align my reads against a fasta containg 1 virus I have the following results:
analysis1
826 reads aligned versus Virus X
If I align my reads against a viral database I have the following results:
analysis2
740 reads aligned versus Virus X
33 reads aligned versus Virux Y
50 reads aligned versus Virux Z
3 reads that are missing (very strange)
Note that I perform the analysis two time, I don't use the same bam/sam file for both alignment (of course).
So I was wondering why bwa is not working in this way:
826 aligned versus Virus X
AND
33 reads against Virus Y
50 reads against Virus Z
Otherwise with a multiple alignment I can miss some data (e.g. analysis2)....right?
Is there something that I'm missing?
Thank you!
Fabio
I'm quite newbie with bioinformatic, so please forgive me if this is a silly question.
Currently I'm align my reads (100bp, single end) against a .fasta containing a list of viruses (ref seq from NCBI). I'm using bwa (sampe)
If I align my reads against a fasta containg 1 virus I have the following results:
analysis1
826 reads aligned versus Virus X
If I align my reads against a viral database I have the following results:
analysis2
740 reads aligned versus Virus X
33 reads aligned versus Virux Y
50 reads aligned versus Virux Z
3 reads that are missing (very strange)
Note that I perform the analysis two time, I don't use the same bam/sam file for both alignment (of course).
So I was wondering why bwa is not working in this way:
826 aligned versus Virus X
AND
33 reads against Virus Y
50 reads against Virus Z
Otherwise with a multiple alignment I can miss some data (e.g. analysis2)....right?
Is there something that I'm missing?
Thank you!
Fabio
Comment