Thanks for the reply! That was my impression; that I wouldn't be able to resolve it with 300bp insert library but only with mate pairs or long read technology.
Cheers,
@ecastron
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by ecastron View PostThanks Brian, I'll give it a try. I anticipate that I'm going to get one cluster because the reads are seemingly identical. It's suggestive that the coverage for the rRNA operon is about 3 times the coverage of the neighboring genes so at a minimum I'll report that in the submission.
I guess the alternative would be going back to the wet lab to check how many copies there are.
Eduardo
Leave a comment:
-
Thanks Brian, I'll give it a try. I anticipate that I'm going to get one cluster because the reads are seemingly identical. It's suggestive that the coverage for the rRNA operon is about 3 times the coverage of the neighboring genes so at a minimum I'll report that in the submission.
I guess the alternative would be going back to the wet lab to check how many copies there are.
Cheers,
Eduardo
Leave a comment:
-
You can try mapping reads to a 16S copy, then clustering the reads that mapped, then assembling the clusters. This will work if the reads are sufficiently long (for Illumina, merging them may be useful) and the 16S are sufficiently different. If not, you'll just get one cluster. You probably need overlapping 2x250bp reads at a minimum (insert size around 400bp+) to have a good chance.
You can cluster like this with Dedupe (packaged with BBMap):
dedupe.sh in=merged.fq -Xmx30g am=f ac=f fo c rnc=f mcs=50 mo=350 pto pattern=cluster_%.fq
The "mo=350" specifies a min overlap of 350bp. This should be around 80%-90% of your read length. If you have single-ended 250bp reads, set it to 200; if you have merged reads with an insert size of around 400bp, try 350. If you have 100bp non-overlapping reads, don't bother, they're too short.
For this kind of situation, which is very sensitive to chimeras, I recommend merging reads with BBMerge using the "vstrict" flag.
Leave a comment:
-
Hi Cyanoevo,
I have the exact same problem. Did you ever find an answer?
Cheers,
Eduardo
Leave a comment:
-
Genes with multiple copies assembling as single contig
Hi all,
I'm doing a denovo assembly of a cyanobacterial genome with SPades, all is working well but when there are multiple copies of a gene (e.g. 16srRNA gene), it appears that all reads associated with that gene are being mapped to a single contig.
Coverage of these contigs appears to correspond quite well to number of expected copies in the genome (i.e. normal coverage ~50x, for a contig with a gene with four copies, coverage ~200x).
Does anyone know of a method to prevent this from happening so that each of the copies assemble separately in different contigs?
Cheers
NTags: None
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 05-14-2024, 07:03 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
05-14-2024, 07:03 AM
|
||
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
37 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
46 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
39 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
Leave a comment: