Thank you!!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Dear RAD/Assembly community,
I was hoping I could pick your brains again regarding my assembly.
I normalized coverage and together with using velvetoptimiser I am quite happy with the results I am getting! For instance, I assembled the reverse reads only, which gave me ~33,000 contigs (this is roughly what I am expecting based on preliminary data) with an N50 of 400. Kmer coverage distribution looks good, too.
However, I now wanted to feed these in as 'long reads' alongside my raw data in velvet to resolve repeats better and connect the forward and reverse reads properly. Weirdly, my N50 goes down to about 380? I have visualized the assembly in tablet, and also mapped back some of my raw data (using BWA) back to check whether forward and reverse reads were actually assembled correctly, and for the few contigs I surveyed by eye this seems to be the case.
I am not sure whether I need to be worried about the decreasing N50, this really seems to be a bit counter-intuitive, as my contigs surely should increase in size by quite a bit when assembling forward and reverse as opposed to just the reverse?
I was also wondering whether there is a good way of quality filtering my contigs from my final assembly. For instance, I only want to keep contigs for future analysis to which both forward and reverse reads map to.
Many thanks in advance for any pointers!!
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
27 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment