Hi all,
OK, after spending quite amount of time reading and researching on aligners, although I am still almost as novice as I was before the reading, I am able to run bowtie and maq with my computer (well, at least in some extent).
In order to help me to learn more about how those aligners work, I ran two experiments like this:
1. run bowtie as instructed in Tutorial with e_coli_1000.fq which is included in bowtie package
The output of this command is
together with a nice output e_coli.bowtie.txt file that I can check what sequence is aligned, where and what the error of that sequence is.
2. run maq easyrun with the same e_coli.fq file. Since the built-in e_coli in bowtie is E_coli_536, I went to NCBI ftp site and downloaded NC_008253.fna. The MAQ run command is:
e_coli.maq.txt file shows
So I have some questions:
a. Why BOWTIE and MAQ gave different results with the same data set (MAQ gave 745 mapped reads and BOWTIE gave 699)? How I can set parameters for both bowtie and maq to get the same results?
b. e_coli.bowtie.txt is a nice text file together with a summary of the mapped reads and errors. How I can check with MAQ output files to have the same summary file, say a file with a summary of mapped reads and their errors?
c. what software I can use for post-alignment analysis? I tried maq mapview but I can only see one mapped read at a time. Is there a software which can show a nice alignment view like BLAT with the error as well as the coordinates of the read on the reference?
Sorry for such a long post and thank you all in advance. Any input will be greatly appreciated.
D.
OK, after spending quite amount of time reading and researching on aligners, although I am still almost as novice as I was before the reading, I am able to run bowtie and maq with my computer (well, at least in some extent).
In order to help me to learn more about how those aligners work, I ran two experiments like this:
1. run bowtie as instructed in Tutorial with e_coli_1000.fq which is included in bowtie package
Code:
~/Desktop/genome/HTdata/e_coli_536$ ../../Bowtie/bowtie-0.9.9.2/bowtie e_coli ../../Bowtie/bowtie-0.9.9.2/reads/e_coli_1000.fq > e_coli.bowtie.txt
Code:
Reported 699 alignments to 1 output stream(s)
2. run maq easyrun with the same e_coli.fq file. Since the built-in e_coli in bowtie is E_coli_536, I went to NCBI ftp site and downloaded NC_008253.fna. The MAQ run command is:
Code:
:~/Desktop/genome/HTdata/e_coli_536$ maq.pl easyrun -d e_coli NC_008253 ../../Bowtie/bowtie-0.9.9.2/reads/e_coli_1000.fq > e_coli.maq.txt
Code:
-- == statmap report == -- # single end (SE) reads: 1000 -- # mapped SE reads: 745 (/ 1000 = 74.5%) -- # paired end (PE) reads: 0 -- # mapped PE reads: 0 (/ 0 = NA%) -- # reads that are mapped in pairs: 0 (/ 0 = NA%) -- # Q>=30 reads that are moved to meet mate-pair requirement: 0 (/ 0 = NA%) -- # Q<30 reads that are moved to meet mate-pair requirement: 0 (NA%)
a. Why BOWTIE and MAQ gave different results with the same data set (MAQ gave 745 mapped reads and BOWTIE gave 699)? How I can set parameters for both bowtie and maq to get the same results?
b. e_coli.bowtie.txt is a nice text file together with a summary of the mapped reads and errors. How I can check with MAQ output files to have the same summary file, say a file with a summary of mapped reads and their errors?
c. what software I can use for post-alignment analysis? I tried maq mapview but I can only see one mapped read at a time. Is there a software which can show a nice alignment view like BLAT with the error as well as the coordinates of the read on the reference?
Sorry for such a long post and thank you all in advance. Any input will be greatly appreciated.
D.
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