I found a way to reconstruct the reference subsequence for an aligned read from the alignment information in SAM file. This is the "MD" field in the output. Here is example:
"MD: A string which summarizes the mismatch positions between the aligned read and the reference genome.
Example:
MD:Z:8G61 indicates a single base pair mismatch. Specifically, the aligned read matches the first 8 bases of the reference, after which it fails to match a G in the reference sequence, followed by 61 exact matches to the reference.
"
Source: http://biobits.org/samtools_primer.html
Thanks for all.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Actually it may not be possible to use something else. Since I am not well familiar with BWA, I am afraid I would not be able to preserve the compatibility with the code when I replace BWA commands with BBmap. Figuring out how to read the reference the way BWA does is the safest way.
Thanks.
Leave a comment:
-
Not a direct answer but if you are open to substituting the aligner then BBMap from BBMap suite is an option. It is written in pure Java and author of BBMap participates (Brian Bushnell) here regularly.
Leave a comment:
-
Thanks!
I will go ahead and check the code.
The problem happens when our code is running, not the BWA. Also, I tried to read the indexing step output files. The large ones are not simple text formate. If that was the case, I would try to input small, tailored reference genomes to see how what is the output from the indexing.
As I noted, our program can handle 1 chromosome without problems. So, I merged the chromosomes of a human genome into one; but BWA exits without indexing the whole genome. The largest single chromosome reference BWA indexed successfully was about 160M bytes.
Leave a comment:
-
I thought BWA (as ends up being the case with a lot of aligners) ends up concatenating the chromosomes together when indexing (with a bunch of N in between). Anyway, BWA at least used to occasionally produce alignments that extended beyond the chromosome bounds, so if you have an example that makes it crash then post that on github as an issue.
Leave a comment:
-
If you are a proficient programmer source code for bwa is available on SF. If you need technical help then you could post to bwa mailing list.
Leave a comment:
-
BWA indexing mechanism
Hi all,
I am new to bioinformatics. I am parallelizing a code that use BWA for alignment.
Can someone please explain to me in general how the indexing is happening?
I ask because the previous coder index and run alignment by calling BWA. then, the code "reads-in the reference geneome"; the code extract subsequence from the read-in reference by using the starting position that appears in the alignment file. For instance;
assume we have the following read: ACCCA
the reference has two chromosomes:
>chr1
GGGGGTTTTT
>chr2
AAACCCCCCCC
and assume the read is aligned to ACCCC in the second chromosome, where the starting position is: 13--I think BWA will produce 13.
the code reads in the reference and stores every chromosomes in a separate data structure. The problem is when when the code gets the subsequence "ACCCA" from the reference, it uses the starting position (13) to extract the subsequence. The way the reference is stored leads to out of range (13 is more than the 11 bases stored in chr2) and the program crashes. and even if the 13 is in range, we will be reading the wrong subsequence.
I need to know the BWA indexing mechanism so I get the correct subsequence from the read-in reference. I tried to add the length prefix to get the correct subsequence, but it did not work, where there are some dependencies in the code that may led to the problem.
Thanks.Tags: None
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
68 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Leave a comment: