I ran FatsQC on a set of 4 Illumina PE exomes and got really weird graphs for the kmer distribution. I've never seen this pattern before - does anyone know what is going on and what to do about it?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I am not entirely sure about what is going on since I don't have the full length Illumina adapter sequences handy, but my guess is that the plot shows an adapter or primer dimer of some sort. Seeing that GGAAG is part of the start of the Illumina adapter (GATCGGAAGAGC..., wihtout the A-tail at the start) and the spacing is always the same this might simply be full-length adapter dimers. Such sequences should not align anywhere, so you probably don't need to worry about them. This doesn't mean that you don't have to trim your sample at all, this is difficult to say without seeing the rest of the plots.
-
removing over-represented sequences does not help
@fkrueger: I found that two TruSeq adaptors were listed among the over-represented sequences in the fastqc report so I removed them for one of the samples and re-ran fastqc. The graph changed somewhat but there are still non-random peaks (below). Any ideas?
Comment
-
I don't know how you removed the adapters, but the k-mers could still result from adapter dimers. Trim Galore for example only removes the entire adapter sequence AGATCGGAAGAGC but only if it starts with the A from the A-tailing process. In your case the sequence seems to start with GATC(GGAAG) and thus wouldn't be affected by adapter trimming.
The CACAC and ACACA is often a highly occurring sequence in MeDIP-Seq or the like. I wouldn't worry too much about the plot for the moment, and only come back to it if you find that you've got an unusually low mapping efficiency or similar.
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
68 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment