Hello,
1)
I have a questions about bowtie's "h_sapiens_37_asm" index.
For the human genome, the concise reference sequences are numbered 0 to 24. I
assume these numbers represent chromosomes. Is 0 chromosome 1? What about X,
Y, and the M?
bowtie -z -f h_sapiens_37asm --concise reads/seq_human.fa human_map
2)
I am also confused about the localization of the 5' end of the read.
According to the dafault output description, the fourth column shows the
"0-based offset into the forward reference strand where leftmost character of
the alignment occurs."
If you don't use the concise option ...
if a read is mapped 5' to 3' from position 1000 to 1035,
the fourth column should be 1000, right?
If a read is mapped 5' to 3' from position 1035 to 1000,
will the fourth column be 1035 or 1000?
I think this means the fourth column will be 1000.
If this is the case, is there an "option" so that I can make it 1035 instead of 1000?
Thanks,
Clayton
1)
I have a questions about bowtie's "h_sapiens_37_asm" index.
For the human genome, the concise reference sequences are numbered 0 to 24. I
assume these numbers represent chromosomes. Is 0 chromosome 1? What about X,
Y, and the M?
bowtie -z -f h_sapiens_37asm --concise reads/seq_human.fa human_map
2)
I am also confused about the localization of the 5' end of the read.
According to the dafault output description, the fourth column shows the
"0-based offset into the forward reference strand where leftmost character of
the alignment occurs."
If you don't use the concise option ...
if a read is mapped 5' to 3' from position 1000 to 1035,
the fourth column should be 1000, right?
If a read is mapped 5' to 3' from position 1035 to 1000,
will the fourth column be 1035 or 1000?
I think this means the fourth column will be 1000.
If this is the case, is there an "option" so that I can make it 1035 instead of 1000?
Thanks,
Clayton
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