I am newbie in NGS. We have sequenced non-model plant through illumina Hiseq 2000, and I preprocessed the raw sequence with fastqc, with fastqc quality check, the sequences passed all the test but failed in "Per Base Sequence Content". What should I do?. In what way I can improve the per base sequence content by quality filtering?. What type of quality filtering/tool should I use?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Can you post an example plot? If one of the items "fails" in FastQC then it does not automatically mean a strike against the dataset.
Here is a recent post of mine with a list of trimming programs/adapter information: http://seqanswers.com/forums/showthread.php?t=40054
-
The question you should be checking into is if there is adapter contamination and/or low quality sequence that you need to remove before the downstream analysis. Some links for various trimming programs are in: http://seqanswers.com/forums/showthread.php?t=40054
Also check post #2 in http://seqanswers.com/forums/showthread.php?t=39889 for an insight into the sequence duplication "problem".
What kind of an experiment is this? It is normal to see that kind of per sequence base content for illumina sequencing.
Comment
-
Is this RNA-seq or genomic sequencing? Can you post a few more details about the expt? What are you going to do afterwards? Assembly?
From what you've posted above, the %AT/%GC looks too uniform (this is how it should be: http://www.bioinformatics.babraham.a...qc_report.html), however, it may not necessarily be an issue.
I don't think there is a trimming issue here, since the ends look fine. You might want to go ahead with the assembly as planned and BLAST the assembled sequences against the NR database in NCBI, just to make sure that they are mapping to sequences close to your species.
Comment
Latest Articles
Collapse
-
by seqadmin
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...-
Channel: Articles
Today, 07:15 AM -
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 08:18 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 08:18 AM
|
||
Started by seqadmin, Today, 08:04 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Today, 08:04 AM
|
||
Started by seqadmin, 06-03-2024, 06:55 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
06-03-2024, 06:55 AM
|
||
Started by seqadmin, 05-30-2024, 03:16 PM
|
0 responses
27 views
0 likes
|
Last Post
by seqadmin
05-30-2024, 03:16 PM
|
Comment