Hellow fellas
I rencently started working on using crossbow to process mouse genome sequence. I am from computer science background and I know quite little about biology
After some experiments and reading through the manual of bowtie, I still didn't get:
1. The command for bowtie is like:
"./bowtie index/index -p 2 --partition $partition_size -X $insert_size -m 1 -v 2 --best --strata --mm --12 --startverbose --mmsweep\"
It is using -m 1 in conjunction with "-best --strata". My understanding is when there's only 1 reportable alignment in the best alignment "stratum", this alignment will be reported.
Bowtie discards alignments when accidentally 2 or more meet the same "best" criteria. is this right?
2. In the output of bowtie, the last second column is called "hit". From the manual:
"this column contains the number of other instances where
the same sequence aligned against the same reference characters as
were aligned against in the reported alignment. This is *not* the
number of other places the read aligns with the same number of
mismatches."
I could not understand this statement. Can any biologist here give me some example of what this means?
Really appreciate if you can help me out here.
Cheers
I rencently started working on using crossbow to process mouse genome sequence. I am from computer science background and I know quite little about biology
After some experiments and reading through the manual of bowtie, I still didn't get:
1. The command for bowtie is like:
"./bowtie index/index -p 2 --partition $partition_size -X $insert_size -m 1 -v 2 --best --strata --mm --12 --startverbose --mmsweep\"
It is using -m 1 in conjunction with "-best --strata". My understanding is when there's only 1 reportable alignment in the best alignment "stratum", this alignment will be reported.
Bowtie discards alignments when accidentally 2 or more meet the same "best" criteria. is this right?
2. In the output of bowtie, the last second column is called "hit". From the manual:
"this column contains the number of other instances where
the same sequence aligned against the same reference characters as
were aligned against in the reported alignment. This is *not* the
number of other places the read aligns with the same number of
mismatches."
I could not understand this statement. Can any biologist here give me some example of what this means?
Really appreciate if you can help me out here.
Cheers
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