I know of a translocation that occurred (I also know the sequence that was translocated) in my sequenced DNA, but I'm not sure where it was translocated to, and the reads of the translocated sequence line up against the reference in the original location. Is there any way to find a translocation using short-reads?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
Hi Agc,
It would help people if you supplied more information;
1) Is it genome re-sequencing or transcriptome data
2) Is it paired end or single reads
3) What is the coverage/number of reads generated
4) What species is it
I don't know if there is a ready made solution for you but my bodge up and leg-it approach would be:
1) Reads that span the translocation won't map to your reference sequence. E.g. Maybe as, for some reads you have, say the first 25bp could map to chromosome 1 and second 25bp to chromosome Y, using human as an example.
2) Assuming my example is similar to your situation, I would take all reads that did not map; for each read here take the first 21bp and the last 21bp of the read and map to genome (maybe with BLAT or BLAST, altering paramters). See which first 21bp and last 21bp map to different chromosomes, there will be your candidate translocation regions but hopefully one stands out as being real (lots of reads mapping to them).
3) Take the sequences of putative translocation, 49bp from each chromosome and make a pseudo translocation sequence BLAST database
4) BLAST all reads against translocation sequences and record those reads that align over full length of the read. The most likely real translocation will have most reads mapping which at least overlap the translocation point by 1 base
This is my rough approach, which will get you the right answer but involves a bit of BLAST, BLAT, Perl/Python magic and some result filtering.
I predict some better experts of NGS know of better/easier solutions, probably with some already developed software. So give it a day or two before embarking my solution.
Good luck.
:-)
ps. If it is paired end, this will help a lot as one mate pair will map to one chromosome and the other mate pair another chromosome (there should be definitely software to help do that) or just parse the SAM output from TopHat or BOWTIE.Last edited by poisson200; 07-22-2010, 04:08 AM.
-
Thanks for the quick reply!
1) Genome re-sequencing
2) Single ~50bp reads
3) Not sure where I can obtain that information.
4) S. Cerevisiae
The translocation occurred within the same chromosome, but I'll try to develop the idea of using the unmapped reads. Although I'd find some sort of ready made solution / any other suggestions very helpful.
Comment
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
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment