Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Thanks for your reply, Brian.
I have mRNA Illumina 100bp paired end reads. I have already removed the adapters, but still have that same the high variation on GC% at the 5' end. For the library prep, TruSeq mRNA prep was used, that's why I am guessing I have the same 5' end bias described before on my dataset. Any thoughts?
Comment
-
BBDuk can trim a set number of bases on the left or right side of a read. However, there are some library-prep protocols that are biased, especially near the read start, and thus have suspicious base-frequency histograms, even though they are correct. So, before you trim, I suggest you map the reads to a reference (even the lowest-quality assembly is OK) to determine whether there is actually a higher error rate in the first X bases of the read. If not, then you should not trim them.
With an assembly, you can determine it like this:
bbmap.sh in=reads.fq mhist=mhist.txt qhist=qhist.txt
This will give you histograms of the average qualities by read position, and match/substitution/insertion/deletion/N rates by read position. That will allow you to determine whether the stated read quality is accurate, and thus whether you need to trim the ends of reads.
If you want to trim a set number of bases on each side, you can use BBDuk's "ftl" (force-trim left) and "ftr" (force-trim right) flags to set the limits of where to trim.
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