I am looking at some other people's processed data at GEO but I am unclear
about the alignment meanings.
Some information about *csfasta.ma files is found in the following guide:
However, I have some questions that were not answered in the manual with
the exception of question #2.
Here is a sample alignment from a single-read, SOLiD csfasta.ma.25.2 file.
T30211102000121023203110321200211210
2_16_1134_F3,chr12.-97446261.1,chr12.75715114.1,chr14.92697281.1
1.
Does the negative sign in front of the chromosomal coordinate indicate a reverse read (- strand)?
2.
Does the .1 in these 3 alignments indicate the number of mismatches as in 1 mismatch each?
3.
For the forward reads, does the coordinate represent the 5' end (the left-most coordinate)?
4.
For the reverse reads, does the coordinate represent the 3' end (the left-most coordinate)?
5.
If the answer to #4 is yes, to obtain the 5' end of the reverse read,
should I add 25 to the coordinate?
For example, to obtain the 5' end of the read in the "chr12.-97446261.1" alignment,
would this be the appropriate operation: 97446261 + 25 = 97446286?
Or should I add 24?
Thanks,
Clayton
about the alignment meanings.
Some information about *csfasta.ma files is found in the following guide:
However, I have some questions that were not answered in the manual with
the exception of question #2.
Here is a sample alignment from a single-read, SOLiD csfasta.ma.25.2 file.
T30211102000121023203110321200211210
2_16_1134_F3,chr12.-97446261.1,chr12.75715114.1,chr14.92697281.1
1.
Does the negative sign in front of the chromosomal coordinate indicate a reverse read (- strand)?
2.
Does the .1 in these 3 alignments indicate the number of mismatches as in 1 mismatch each?
3.
For the forward reads, does the coordinate represent the 5' end (the left-most coordinate)?
4.
For the reverse reads, does the coordinate represent the 3' end (the left-most coordinate)?
5.
If the answer to #4 is yes, to obtain the 5' end of the reverse read,
should I add 25 to the coordinate?
For example, to obtain the 5' end of the read in the "chr12.-97446261.1" alignment,
would this be the appropriate operation: 97446261 + 25 = 97446286?
Or should I add 24?
Thanks,
Clayton