Open ezioljj opened 2 years ago
Hello,
Can you try adding --score-min G,1,10
to your command line when using v2.3 or later? Please let me know if this affects your alignment rate.
Hi,
Thank you for this kind help, it worked. However, the mapping rate between v2.2 and v2.3 are different, here are detailed results:
v2.3: 250000 reads; of these: 250000 (100.00%) were unpaired; of these: 37118 (14.85%) aligned 0 times 54109 (21.64%) aligned exactly 1 time 158773 (63.51%) aligned >1 times 85.15% overall alignment rate v2.2: 250000 reads; of these: 250000 (100.00%) were unpaired; of these: 27169 (10.87%) aligned 0 times 37352 (14.94%) aligned exactly 1 time 185479 (74.19%) aligned >1 times 89.13% overall alignment rate
I would like to know why
--score-min G,1,10
leads to this successful mapping in v2.3? and why v2.2 and v2.3 exhibited different mapping rate? Best regards,Hello,
Can you try adding
--score-min G,1,10
to your command line when using v2.3 or later? Please let me know if this affects your alignment rate.
This change was highlighted in the release notes for v2.3.1
* The default `--score-min` for `--local` mode is now `G,20,8`.
That was the stated default in the documentation for a while,
but the actual default was `G,0,10` for many versions. Now the
default matches the documentation and, we find, yields more
accurate alignments than `G,0,10`
I wanted confirmation from you before letting the cat out of the bag.
This change was highlighted in the release notes for v2.3.1
* The default `--score-min` for `--local` mode is now `G,20,8`. That was the stated default in the documentation for a while, but the actual default was `G,0,10` for many versions. Now the default matches the documentation and, we find, yields more accurate alignments than `G,0,10`
I wanted confirmation from you before letting the cat out of the bag.
Thank you for this explanation. I stilll have one question, what is the actual meaning of the 1
in G,1,10
, and what is the actual meaning of the 10
. (in my case, the reads used for mapping ranged from 17-21 bp, which is very short).
best regards,
From the manual:
Setting function options
Some Bowtie 2 options specify a function rather than an individual number or setting. In these cases the user specifies three parameters: (a) a function type F, (b) a constant term B, and (c) a coefficient A. The available function types are constant (C), linear (L), square-root (S), and natural log (G). The parameters are specified as F,B,A - that is, the function type, the constant term, and the coefficient are separated by commas with no whitespace. The constant term and coefficient may be negative and/or floating-point numbers.
For example, if the function specification is L,-0.4,-0.6, then the function defined is:
f(x) = -0.4 + -0.6 * x
If the function specification is G,1,5.4, then the function defined is:
f(x) = 1.0 + 5.4 * ln(x)
See the documentation for the option in question to learn what the parameter x is for. For example, in the case if the --score-min option, the function f(x) sets the minimum alignment score necessary for an alignment to be considered valid, and x is the read length.
From the manual:
Setting function options
Some Bowtie 2 options specify a function rather than an individual number or setting. In these cases the user specifies three parameters: (a) a function type F, (b) a constant term B, and (c) a coefficient A. The available function types are constant (C), linear (L), square-root (S), and natural log (G). The parameters are specified as F,B,A - that is, the function type, the constant term, and the coefficient are separated by commas with no whitespace. The constant term and coefficient may be negative and/or floating-point numbers.
For example, if the function specification is L,-0.4,-0.6, then the function defined is:
f(x) = -0.4 + -0.6 * x
If the function specification is G,1,5.4, then the function defined is:
f(x) = 1.0 + 5.4 * ln(x)
See the documentation for the option in question to learn what the parameter x is for. For example, in the case if the --score-min option, the function f(x) sets the minimum alignment score necessary for an alignment to be considered valid, and x is the read length.
Thank you very much for this kind and professional guidance.
Hi,
I used old version (2.2.5) for mapping, and I got around 90% overall alignment rate. However, when I used new version, I could only get overall alignment rate less than 0.1%. I used the same fastq files, index and commands, I would like to know if any fundamental changes between different version has led to this issue? (samtools version are same, version 1.9)
best regards
The following are detailed information: